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3it8

Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein

Method: X-RAY DIFFRACTION Dmax: 201.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tumor necrosis factor

Homo sapiens

UniProt P01375

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 82–233 Chain B； UniProt 82–233 Chain C； UniProt 82–233 Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233 2L protein × 3 （Q9DHW0） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium citrate, 0.2M NaBr, pH 5.5, vapor diffusion, hanging drop, temperature 298K Resolution 2.80 Å R-free 0.266
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain G； UniProt 82–233 Chain H； UniProt 82–233 Chain I； UniProt 82–233 Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233 2L protein × 3 （Q9DHW0） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium citrate, 0.2M NaBr, pH 5.5, vapor diffusion, hanging drop, temperature 298K Resolution 2.80 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3IT8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A8M TUMOR NECROSIS FACTOR ALPHA, R31D MUTANT Deposited 1998-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Mutation：R31D Mutation：R31D Mutation：R31D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；CRYSTALLIZED FROM 88% MGSO4, 1-2% PEG 400, 0.2 M MES, PH 5.5.
Resolution 2.30 Å R-free 0.240
1TNF THE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT 2.6 ANGSTROMS RESOLUTION. IMPLICATIONS FOR RECEPTOR BINDING Deposited 1989-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
21TV Cryo-EM structure of the TNF-alpha-Ozoralizumab (OZR)-HSA complex Deposited 2025-12-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Chain D 77–233（157 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.19 Å
21TW Cryo-EM structure of TNF-alpha in complex with two anti-TNF-alpha nanobodies, TNF30, derived from the TNF-alpha inhibitor Ozoralizumab (OZR) Deposited 2025-12-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Chain D 77–233（157 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.43 Å
2AZ5 Crystal Structure of TNF-alpha with a small molecule inhibitor Deposited 2005-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 86–233（148 aa）
Chain B 86–233（148 aa）
Chain C 86–233（148 aa）
Chain D 86–233（148 aa）
Not recorded 307 6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-(TRIFLUOROMETHYL)PHENYL]-1H-INDOL-3-YL}METHYL)AMINO]ETHYL}AMINO)METHYL]-4H-CHROMEN-4-ONE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2.5 M Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.278
2E7A TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity Deposited 2007-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Mutation：K11M, K65S, A84S, V85T, S86T, Y87H, Q88N, T89Q, K90P, K98R, K112N, K128P Mutation：K11M, K65S, A84S, V85T, S86T, Y87H, Q88N, T89Q, K90P, K98R, K112N, K128P Mutation：K11M, K65S, A84S, V85T, S86T, Y87H, Q88N, T89Q, K90P, K98R, K112N, K128P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.05M HEPES pH7.5, 1.5%(w/v) 1,2,3-Heptanetriol, 12.5% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.239
2TUN CONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROSIS FACTOR Deposited 1993-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Mutation：A84V Mutation：A84V Mutation：A84V Mutation：A84V Mutation：A84V Mutation：A84V No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.10 Å
2TUN CONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROSIS FACTOR Deposited 1993-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Mutation：A84V Mutation：A84V Mutation：A84V No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.10 Å
2TUN CONFORMATIONAL CHANGES IN THE (ALA-84-VAL) MUTANT OF TUMOR NECROSIS FACTOR Deposited 1993-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Mutation：A84V Mutation：A84V Mutation：A84V No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.10 Å
2ZJC TNFR1 selectve TNF mutant; R1-6 Deposited 2008-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa） Fragment：R1-6, UNP residues 77-233
Chain B 77–233（157 aa） Fragment：R1-6, UNP residues 77-233
Chain C 77–233（157 aa） Fragment：R1-6, UNP residues 77-233
Mutation：K11M, K65S, L29K, R31A, R32G, K90P, K98R, K112N, K128P, E146S, S147T Mutation：K11M, K65S, L29K, R31A, R32G, K90P, K98R, K112N, K128P, E146S, S147T Mutation：K11M, K65S, L29K, R31A, R32G, K90P, K98R, K112N, K128P, E146S, S147T GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH6.5
Resolution 2.50 Å R-free 0.272
2ZPX TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity; R1antTNF-T8 Deposited 2008-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa） Fragment：UNP residues 77-233
Chain B 77–233（157 aa） Fragment：UNP residues 77-233
Chain C 77–233（157 aa） Fragment：UNP residues 77-233
Mutation：K11M, K65S, A84T, V85P, S86A, Y87I, Q88N, T89R, K90P, K98R, K112N, K128P Mutation：K11M, K65S, A84T, V85P, S86A, Y87I, Q88N, T89R, K90P, K98R, K112N, K128P Mutation：K11M, K65S, A84T, V85P, S86A, Y87I, Q88N, T89R, K90P, K98R, K112N, K128P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG1500, 0.2M Calcium Acetate, 0.1M Sodium Cacodylate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.83 Å R-free 0.309
3ALQ Crystal structure of TNF-TNFR2 complex Deposited 2010-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 77–233（157 aa） Fragment：soluble form
Chain B 77–233（157 aa） Fragment：soluble form
Chain C 77–233（157 aa） Fragment：soluble form
Mutation：K11M, K65S, K90P, K98R, K112N, K128P Mutation：K11M, K65S, K90P, K98R, K112N, K128P Mutation：K11M, K65S, K90P, K98R, K112N, K128P CO COBALT (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.281
3ALQ Crystal structure of TNF-TNFR2 complex Deposited 2010-08-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 77–233（157 aa） Fragment：soluble form
Chain E 77–233（157 aa） Fragment：soluble form
Chain F 77–233（157 aa） Fragment：soluble form
Mutation：K11M, K65S, K90P, K98R, K112N, K128P Mutation：K11M, K65S, K90P, K98R, K112N, K128P Mutation：K11M, K65S, K90P, K98R, K112N, K128P CO COBALT (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.00 Å R-free 0.281
3L9J Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal structure of the antagonist-TNFalpha complex Deposited 2010-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 85–233（149 aa） Fragment：UNP residues 85-233
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 0.35M MgAc, 20% 2-propanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.10 Å R-free 0.217
3WD5 Crystal structure of TNFalpha in complex with Adalimumab Fab fragment Deposited 2013-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa） Fragment：Tumor necrosis factor, soluble form
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；30% PEG400, 0.1M sodium acetate trihydrate, 0.1M cadmium chloride hydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 3.10 Å R-free 0.275
4G3Y Crystal structure of TNF-alpha in complex with Infliximab Fab fragment Deposited 2012-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 77–233（157 aa） Fragment：Tumor necrosis factor, soluble form
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；1.0M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.235
4G3Y Crystal structure of TNF-alpha in complex with Infliximab Fab fragment Deposited 2012-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 77–233（157 aa） Fragment：Tumor necrosis factor, soluble form
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；1.0M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.235
4TSV HIGH RESOLUTION CRYSTAL STRUCTURE OF A HUMAN TNF-ALPHA MUTANT Deposited 1997-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 84–233（150 aa）
Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；1.4 M SODIUM FORMATE, pH 6.8
Resolution 1.80 Å R-free 0.262
4TWT Human TNFa dimer in complex with the semi-synthetic bicyclic peptide M21 Deposited 2014-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric
Chain A 77–233（157 aa） Fragment：UNP Residues 77-233
Chain B 77–233（157 aa） Fragment：UNP Residues 77-233
Not recorded GOL GLYCEROL × 4 38A (2,4,6-trimethylbenzene-1,3,5-triyl)trimethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25.5% PEG 8000, 0.085 M Na Cacodylate pH 6.5, 0.17M Ammonium Sulfate, 15% Glycerol.
Resolution 2.85 Å R-free 0.286
4TWT Human TNFa dimer in complex with the semi-synthetic bicyclic peptide M21 Deposited 2014-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: Trimeric
Chain C 77–233（157 aa） Fragment：UNP Residues 77-233
Chain D 77–233（157 aa） Fragment：UNP Residues 77-233
Not recorded GOL GLYCEROL × 2 38A (2,4,6-trimethylbenzene-1,3,5-triyl)trimethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25.5% PEG 8000, 0.085 M Na Cacodylate pH 6.5, 0.17M Ammonium Sulfate, 15% Glycerol.
Resolution 2.85 Å R-free 0.286
5M2I Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1 Deposited 2016-10-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；mixed 100 nL of protein 8 mg per ml in HEPES 10 mM pH 7.0 with 100 nL of precipitant solution containing 20% PEG3000 and 0.2M NaCl and 0.1M HEPES at pH 7.5.
Resolution 2.15 Å R-free 0.238
5M2I Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1 Deposited 2016-10-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；mixed 100 nL of protein 8 mg per ml in HEPES 10 mM pH 7.0 with 100 nL of precipitant solution containing 20% PEG3000 and 0.2M NaCl and 0.1M HEPES at pH 7.5.
Resolution 2.15 Å R-free 0.238
5M2J Complex between human TNF alpha and Llama VHH2 Deposited 2016-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 to 300 nL of protein at 11 mg per ml in HEPES 10 mM pH 7.0 with 100 nL of precipitant solution containing 12% 130 mM NaCl and 366 mM CaCl2 and 70 mM CAPS pH 9.0 and 30 mM MES pH 8.0
Resolution 1.90 Å R-free 0.196
5M2M Complex between human TNF alpha and Llama VHH3 Deposited 2016-10-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；mixing 100 to 300 nL of protein (9 mg per ml in HEPES 10 mM pH 7.0) with 100 nL of precipitant solution containing: 9% PEG3350, 8% PEG-MME550, 130 mM NaSO4, 70 mM BTP, 30 mM Mes, and 3 mM ZnSO4, 8.5
Resolution 2.30 Å R-free 0.247
5M2M Complex between human TNF alpha and Llama VHH3 Deposited 2016-10-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 77–233（157 aa）
Chain I 77–233（157 aa）
Chain M 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；mixing 100 to 300 nL of protein (9 mg per ml in HEPES 10 mM pH 7.0) with 100 nL of precipitant solution containing: 9% PEG3350, 8% PEG-MME550, 130 mM NaSO4, 70 mM BTP, 30 mM Mes, and 3 mM ZnSO4, 8.5
Resolution 2.30 Å R-free 0.247
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 77–233（157 aa） Fragment：UNP residues 77-233
Chain B 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain T 77–233（157 aa） Fragment：UNP residues 77-233
Chain U 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain V 77–233（157 aa） Fragment：UNP residues 77-233
Chain W 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 77–233（157 aa） Fragment：UNP residues 77-233
Chain Y 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 13 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain Z 77–233（157 aa） Fragment：UNP residues 77-233
Chain a 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 14 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain b 77–233（157 aa） Fragment：UNP residues 77-233
Chain c 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 15 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain d 77–233（157 aa） Fragment：UNP residues 77-233
Chain e 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 16 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain f 77–233（157 aa） Fragment：UNP residues 77-233
Chain g 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 17 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain h 77–233（157 aa） Fragment：UNP residues 77-233
Chain i 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 18 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain j 77–233（157 aa） Fragment：UNP residues 77-233
Chain k 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 19 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain l 77–233（157 aa） Fragment：UNP residues 77-233
Chain m 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 77–233（157 aa） Fragment：UNP residues 77-233
Chain D 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 20 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain n 77–233（157 aa） Fragment：UNP residues 77-233
Chain o 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 21 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain p 77–233（157 aa） Fragment：UNP residues 77-233
Chain q 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 22 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain r 77–233（157 aa） Fragment：UNP residues 77-233
Chain s 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 23 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain t 77–233（157 aa） Fragment：UNP residues 77-233
Chain u 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 24 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain v 77–233（157 aa） Fragment：UNP residues 77-233
Chain w 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain F 77–233（157 aa） Fragment：UNP residues 77-233
Chain G 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain H 77–233（157 aa） Fragment：UNP residues 77-233
Chain I 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain J 77–233（157 aa） Fragment：UNP residues 77-233
Chain K 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain L 77–233（157 aa） Fragment：UNP residues 77-233
Chain M 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain N 77–233（157 aa） Fragment：UNP residues 77-233
Chain O 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain P 77–233（157 aa） Fragment：UNP residues 77-233
Chain Q 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5MU8 HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 Deposited 2017-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain R 77–233（157 aa） Fragment：UNP residues 77-233
Chain S 77–233（157 aa） Fragment：UNP residues 77-233
Not recorded JNI ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG
Resolution 3.00 Å R-free 0.300
5TSW HIGH RESOLUTION CRYSTAL STRUCTURE OF A HUMAN TNF-ALPHA MUTANT Deposited 1999-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 84–233（150 aa）
Chain B 84–233（150 aa）
Chain C 84–233（150 aa）
Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；20% POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.6, pH 6.8
Resolution 2.50 Å R-free 0.299
5TSW HIGH RESOLUTION CRYSTAL STRUCTURE OF A HUMAN TNF-ALPHA MUTANT Deposited 1999-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 84–233（150 aa）
Chain E 84–233（150 aa）
Chain F 84–233（150 aa）
Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F Mutation：DELETION OF N-TERMINAL SEVEN RESIDUES, L29S, S52I, Y56F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；20% POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM CITRATE PH 5.6, pH 6.8
Resolution 2.50 Å R-free 0.299
5UUI Crystal Structure of Spin-Labeled T77C TNFa Deposited 2017-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Not recorded MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；TNFa (VCID10616, B114005) at 10 mg/ml (in 10 mM HEPES, pH = 7.5, 150 mM NaCl) was mixed with an equal volume of protein solution and a solution containing 24% (w/v) PEG-4000, 0.24 M MgCl2, 0.05% DDM, and 0.1 M HEPES/NaOH, pH=8.5. Crystals were produced by sitting drop vapor diffusion at 16 degrees Celsius. Crystals were then soaked with the same solution supplemented with 10% MTSL for one week and harvested with paraffin oil.
Resolution 1.40 Å R-free 0.170
5YOY Crystal structure of the human tumor necrosis factor in complex with golimumab Fv Deposited 2017-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium acetate trihydrate pH 4.6, 1.4M sodium chloride
Resolution 2.73 Å R-free 0.234
5YOY Crystal structure of the human tumor necrosis factor in complex with golimumab Fv Deposited 2017-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain J 77–233（157 aa）
Chain K 77–233（157 aa）
Chain L 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium acetate trihydrate pH 4.6, 1.4M sodium chloride
Resolution 2.73 Å R-free 0.234
6OOY Asymmetric hTNF-alpha Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 A7M {1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；13% MPD, 13% PEG 1000, 13% PEG 3350, 0.1M HEPES, PH 8.0,VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Resolution 2.50 Å R-free 0.272
6OOZ Asymmetric hTNF-alpha Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded CL CHLORIDE ION × 1 A6Y (S)-{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}(pyridin-4-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；10% PEG 2000, 15% PEG 3350, 3% XYLITOL, 0.1 M HEPES, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Resolution 2.80 Å R-free 0.273
6OP0 Asymmetric hTNF-alpha Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded A7A (R)-{1-[(2,5-dimethylphenyl)methyl]-6-(1-methyl-1H-pyrazol-4-yl)-1H-benzimidazol-2-yl}(pyridin-4-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；23.2% PEG 3350, 5% MPD, 100 MM TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Resolution 2.55 Å R-free 0.244
6RMJ Crystal structure of human NGR-TNF Deposited 2019-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Mutation：N-terminal fusion with CNGRCG peptide Mutation：N-terminal fusion with CNGRCG peptide Mutation：N-terminal fusion with CNGRCG peptide No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；50 mM MES, 2.8 M magnesium sulfate, 1 M NaCL, 2% isopropanol
Resolution 2.65 Å R-free 0.253
6X81 Crystal Structure of TNFalpha with isoquinoline compound 2 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded UTJ [4-(isoquinolin-8-yl)phenyl]acetonitrile × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M Magnesium acetate, 0.05 M sodium cacodylate, pH 6.5
Resolution 2.81 Å R-free 0.231
6X81 Crystal Structure of TNFalpha with isoquinoline compound 2 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded UTJ [4-(isoquinolin-8-yl)phenyl]acetonitrile × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M Magnesium acetate, 0.05 M sodium cacodylate, pH 6.5
Resolution 2.81 Å R-free 0.231
6X82 Crystal Structure of TNFalpha with isoquinoline compound 4 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded UTM 8-[4-(2-{5-[(4-methylpiperazin-1-yl)methyl]-2-(1H-pyrrolo[3,2-c]pyridin-3-yl)phenoxy}ethyl)phenyl]isoquinoline × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M Magnesium acetate, 0.05M sodium cacodylate, pH 6.5
Resolution 2.75 Å R-free 0.230
6X82 Crystal Structure of TNFalpha with isoquinoline compound 4 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded UTM 8-[4-(2-{5-[(4-methylpiperazin-1-yl)methyl]-2-(1H-pyrrolo[3,2-c]pyridin-3-yl)phenoxy}ethyl)phenyl]isoquinoline × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M Magnesium acetate, 0.05M sodium cacodylate, pH 6.5
Resolution 2.75 Å R-free 0.230
6X83 Crystal Structure of TNFalpha with fragment compound 6 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded UTS 1-benzyl-1H-benzimidazole × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M magnesium acetate, 0.05M sodium cacodylate, pH 6.5
Resolution 2.83 Å R-free 0.261
6X83 Crystal Structure of TNFalpha with fragment compound 6 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded UTS 1-benzyl-1H-benzimidazole × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M magnesium acetate, 0.05M sodium cacodylate, pH 6.5
Resolution 2.83 Å R-free 0.261
6X85 Crystal Structure of TNFalpha with indolinone compound 9 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded UTV 1-{[2-(difluoromethoxy)phenyl]methyl}-2,2-dimethyl-1,2-dihydro-3H-indol-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG 8000, 0.2M magnesium acetate, 0.05M sodium cacodylate, pH 6.5
Resolution 2.85 Å R-free 0.252
6X85 Crystal Structure of TNFalpha with indolinone compound 9 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG 8000, 0.2M magnesium acetate, 0.05M sodium cacodylate, pH 6.5
Resolution 2.85 Å R-free 0.252
6X86 Crystal Structure of TNFalpha with indolinone compound 11 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded UTY 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M magnesium acetate, 0.05M sodium cacadylate, pH 6.5
Resolution 2.93 Å R-free 0.244
6X86 Crystal Structure of TNFalpha with indolinone compound 11 Deposited 2020-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded UTY 3-[(6-{2-[(3R)-4-(hydroxyacetyl)-3-methylpiperazin-1-yl]pyrimidin-5-yl}-2,2-dimethyl-3-oxo-2,3-dihydro-1H-indol-1-yl)methyl]pyridine-2-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；15% PEG8000, 0.2M magnesium acetate, 0.05M sodium cacadylate, pH 6.5
Resolution 2.93 Å R-free 0.244
7ASY Transmembrane helix of tumor necrosis factor alpha in trifluorethanol Deposited 2020-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–60（33 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.5 mM TNFA_WT_TM, trifluoroethanol/water | trifluoroethanol/water
Resolution not provided
7AT7 Transmembrane helix of tumor necrosis factor alpha in trifluorethanol, S34P mutant Deposited 2020-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–60（33 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.5 mM TNFa_TM_S34P, trifluoroethanol/water | trifluoroethanol/water
Resolution not provided
7ATB Transmembrane helix of tumor necrosis factor alpha in trifluorethanol, AGALLL mutant Deposited 2020-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–60（33 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 0.5 mM TNFA_TM_AGALLL, trifluoroethanol/water | trifluoroethanol/water
Resolution not provided
7JRA HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quinolin-6-yl)pyrimidin-2-yl]propan-2-ol Deposited 2020-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Mutation：YES Mutation：YES Mutation：YES VGY 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quinolin-6-yl)pyrimidin-2-yl]propan-2-ol × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100 mM HEPES, pH 7.5, 13% (w/v) MePEG5000, 3% (v/v) dioxane
Resolution 2.10 Å R-free 0.235
7KP9 asymmetric hTNF-alpha Deposited 2020-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded A7G 1-{[2-(difluoromethoxy)phenyl]methyl}-2-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-benzimidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；21.44% PEG 3350, 100 mM Tris pH9.0, vapor diffusion, temperature 298K
Resolution 2.15 Å R-free 0.241
7KPA asymmetric hTNF-alpha Deposited 2020-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded D84 5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；24.4% PEG 3350, 100 mM HEPES, pH7.0
Resolution 2.30 Å R-free 0.262
7KPB Human TNF-alpha TNFR1 complex bound to conformationally selective antibody Deposited 2020-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Mutation：N25D, C153S Mutation：N25D, C153S Mutation：N25D, C153S GOL GLYCEROL × 9 D84 5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；0.1M HEPES, pH7.0, 10% w/v PEG6,000 and cryo-protected in glycerol performed in 5-10-15% steps. Vapor diffusion, sitting drop, temperature 289K
Resolution 3.00 Å R-free 0.256
7QLF Conformational ensemble of solnatide in solution Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 178–191（14 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5；290 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 1 mM solnatide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7TA3 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by alpha-peptide-3 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；1.5M ammonium sulfate, 0.1 M tris HCL pH 8.5, 12% glycerol
Resolution 2.50 Å R-free 0.277
7TA3 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by alpha-peptide-3 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–233（157 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；1.5M ammonium sulfate, 0.1 M tris HCL pH 8.5, 12% glycerol
Resolution 2.50 Å R-free 0.277
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 77–233（157 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–233（157 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 77–233（157 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–233（157 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 77–233（157 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 77–233（157 aa）
Not recorded NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 77–233（157 aa）
Not recorded NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
7TA6 Trimer-to-Monomer Disruption of Tumor Necrosis Factor-alpha (TNF-alpha) by unnatural alpha/beta-peptide-1 Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 77–233（157 aa）
Not recorded K POTASSIUM ION × 1 NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.8 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 4% ethylene glycol
Resolution 2.67 Å R-free 0.273
8Z8M Crystal structure of human TNF alpha in complex with TNF30(VHH) domain of ozoralizumab Deposited 2024-04-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 77–233（157 aa） Fragment：UNP residues 76-232
Chain C 77–233（157 aa） Fragment：UNP residues 76-232
Chain E 77–233（157 aa） Fragment：UNP residues 76-232
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.03M Diethylene glycol; 0.03M Triethylene glycol; 0.03M Tetraethylene glycol; 0.03M Pentaethylene glycol 0.05M Sodium HEPES; 0.05M MOPS pH7.5 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350
Resolution 2.59 Å R-free 0.269
8Z8M Crystal structure of human TNF alpha in complex with TNF30(VHH) domain of ozoralizumab Deposited 2024-04-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 77–233（157 aa） Fragment：UNP residues 76-232
Chain I 77–233（157 aa） Fragment：UNP residues 76-232
Chain K 77–233（157 aa） Fragment：UNP residues 76-232
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.03M Diethylene glycol; 0.03M Triethylene glycol; 0.03M Tetraethylene glycol; 0.03M Pentaethylene glycol 0.05M Sodium HEPES; 0.05M MOPS pH7.5 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350
Resolution 2.59 Å R-free 0.269
8ZUI Binary cluster of TNF-TNFR1 ectodomain complex Deposited 2024-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Chain G 77–233（157 aa）
Chain H 77–233（157 aa）
Chain I 77–233（157 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.56 Å
9BN7 X-ray crystal structure of TNFa-VNAR C4 complex Deposited 2024-05-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 6 NI NICKEL (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；RD22EH38, D5.1 0.1M MES, pH 6, 0.1M magnesium chloride, 8% w/v polyethylene glycol 6000
Resolution 1.92 Å R-free 0.245
9DJW X-ray crystal structure of TNFa-VNAR D1 complex Deposited 2024-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric
Chain 2 78–233（156 aa）
Chain 3 78–233（156 aa）
Chain 4 78–233（156 aa）
Chain A 78–233（156 aa）
Chain B 78–233（156 aa）
Chain C 78–233（156 aa）
Chain G 78–233（156 aa）
Chain H 78–233（156 aa）
Chain I 78–233（156 aa）
Chain M 78–233（156 aa）
Chain N 78–233（156 aa）
Chain O 78–233（156 aa）
Chain S 78–233（156 aa）
Chain T 78–233（156 aa）
Chain U 78–233（156 aa）
Chain Y 78–233（156 aa）
Chain Z 78–233（156 aa）
Chain a 78–233（156 aa）
Chain e 78–233（156 aa）
Chain f 78–233（156 aa）
Chain g 78–233（156 aa）
Chain k 78–233（156 aa）
Chain l 78–233（156 aa）
Chain m 78–233（156 aa）
Chain q 78–233（156 aa）
Chain r 78–233（156 aa）
Chain s 78–233（156 aa）
Chain w 78–233（156 aa）
Chain x 78–233（156 aa）
Chain y 78–233（156 aa）
Not recorded GOL GLYCEROL × 17 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；19 % PEG 8000, 0.2 M ammonium sulphate and 0.1 M MES pH 6.0
Resolution 3.43 Å R-free 0.288
9OJO Crystal structure of TNF alpha in complex with compound 1 Deposited 2025-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded A1CB1 2-{5-[(1S,10S)-1-phenyl-1,2,3,4-tetrahydropyrido[1,2-a][1,3]benzimidazol-8-yl]pyrimidin-2-yl}propan-2-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；296 K；30% (w/v) PEG 1000, 0.1M Tris pH 8.5
Resolution 1.36 Å R-free 0.217
9OJS Crystal structure of TNF alpha in complex with compound 4 Deposited 2025-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded A1CB0 (6R,13R,14R)-10-fluoro-11-[2-(2-hydroxypropan-2-yl)pyrimidin-5-yl]-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-5(14H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；296 K；30% (w/v) PEG 1000, 0.1 M HEPES pH 7.5
Resolution 1.85 Å R-free 0.245
9OJY Crystal structure of TNF alpha in complex with compound 3. Deposited 2025-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded A1CBZ (6R,13R,14S)-1-(difluoromethoxy)-11-[2-(2-hydroxypropan-2-yl)pyrimidin-5-yl]-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-5(14H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；296 K；20% (w/v) PEG 3000, 0.1M Tris pH 7.0, 0.2M calcium acetate.
Resolution 2.16 Å R-free 0.253
9OJY Crystal structure of TNF alpha in complex with compound 3. Deposited 2025-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded A1CBZ (6R,13R,14S)-1-(difluoromethoxy)-11-[2-(2-hydroxypropan-2-yl)pyrimidin-5-yl]-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-5(14H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；296 K；20% (w/v) PEG 3000, 0.1M Tris pH 7.0, 0.2M calcium acetate.
Resolution 2.16 Å R-free 0.253
9OK6 Crystal structure of TNF alpha in complex with compound 19 Deposited 2025-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 77–233（157 aa）
Chain B 77–233（157 aa）
Chain C 77–233（157 aa）
Not recorded A1CCE (4S,8aR)-7-{5-[(6R,13R,14S)-5,14-dihydro-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-11-yl]pyrimidin-2-yl}hexahydroimidazo[1,5-a]pyrazin-3(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；296 K；20% (w/v) PEG 8000, 0.1M sodium cacodylate pH 6.5, 0.2M magnesium acetate.
Resolution 2.78 Å R-free 0.241
9OK6 Crystal structure of TNF alpha in complex with compound 19 Deposited 2025-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 77–233（157 aa）
Chain E 77–233（157 aa）
Chain F 77–233（157 aa）
Not recorded A1CCE (4S,8aR)-7-{5-[(6R,13R,14S)-5,14-dihydro-7H-6,14-methanopyrido[3',2':4,5]imidazo[1,2-b][2,5]benzodiazocin-11-yl]pyrimidin-2-yl}hexahydroimidazo[1,5-a]pyrazin-3(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；296 K；20% (w/v) PEG 8000, 0.1M sodium cacodylate pH 6.5, 0.2M magnesium acetate.
Resolution 2.78 Å R-free 0.241

49 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TNFA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–161； UniProt 82–233 Author chain B； PDBConstruct 10–161； UniProt 82–233 Author chain C； PDBConstruct 10–161； UniProt 82–233 Author chain G； PDBConstruct 10–161； UniProt 82–233 Author chain H； PDBConstruct 10–161； UniProt 82–233 Author chain I； PDBConstruct 10–161； UniProt 82–233

2L protein

Yaba-like disease virus

UniProt Q9DHW0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain D； UniProt 17–332 Chain E； UniProt 17–332 Chain F； UniProt 17–332 Not recorded Tumor necrosis factor × 3 （P01375） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium citrate, 0.2M NaBr, pH 5.5, vapor diffusion, hanging drop, temperature 298K Resolution 2.80 Å R-free 0.266
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain J； UniProt 17–332 Chain K； UniProt 17–332 Chain L； UniProt 17–332 Not recorded Tumor necrosis factor × 3 （P01375） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 6000, sodium citrate, 0.2M NaBr, pH 5.5, vapor diffusion, hanging drop, temperature 298K Resolution 2.80 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q9DHW0_YLDV
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–316； UniProt 17–332 Author chain E； PDBConstruct 1–316； UniProt 17–332 Author chain F； PDBConstruct 1–316； UniProt 17–332 Author chain J； PDBConstruct 1–316； UniProt 17–332 Author chain K； PDBConstruct 1–316； UniProt 17–332 Author chain L； PDBConstruct 1–316； UniProt 17–332

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3it8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3it8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3it8
Deposition date deposition_date2009-08-27
Structure title titleCrystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein
Keywords keywords;MHC CLASS I HOMOLOG, Cell membrane, Cytokine, Disulfide bond, Glycoprotein, Lipoprotein, Membrane, Myristate, Phosphoprotein, Secreted, Signal-anchor, Transmembrane, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier58.87 Å
Radius of gyration Rg (electron density) rg_electron58.63 Å
Forward intensity I(0) i01342070000.00
Molecular weight molecular_weight310460.0 kDa
Excluded volume excluded_volume389140 ų
Envelope volume envelope_volume583460 ų
Hydration-shell volume shell_volume83562 ų
Envelope diameter envelope_diameter208.5 Å
Shell Rg shell_rg60.01 Å
Envelope Rg envelope_rg57.11 Å
Shape Rg shape_rg58.59 Å
Total Rg total_rg58.78 Å
Total atoms total_atoms21906
Residues n_residues2706
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax201.8 Å
Rg (real space) rg_real59.03 Å
Rg uncertainty (real space) rg_real_error1.94 Å
I(0) (real space) i0_real1.3420e+09
I(0) uncertainty (real space) i0_real_error2.8710e+07
Rg (reciprocal space) rg_reciprocal58.70 Å
I(0) (reciprocal space) i0_reciprocal1341000000.0000
Solution quality estimate total_estimate0.8693
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.3 Å
Skewness Skewness skewness0.323
Kurtosis Kurtosis kurtosis-0.557
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56840000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.710
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3it8a_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like
Domain ID domain_idd3it8b_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like
Domain ID domain_idd3it8c_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like
Domain ID domain_idd3it8g_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like
Domain ID domain_idd3it8h_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like
Domain ID domain_idd3it8i_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like

CATH v4.4 (18 domains)

Domain ID domain_id3it8A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3it8B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3it8C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3it8D01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3it8D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3it8E01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3it8E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3it8F01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3it8F02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3it8G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3it8H00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3it8I00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3it8J01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3it8J02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3it8K01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3it8K02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3it8L01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3it8L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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9. Files and Curves (10)