6x85

Crystal Structure of TNFalpha with indolinone compound 9

Method: X-RAY DIFFRACTION D_max: 99.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tumor necrosis factor

Homo sapiens

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 77–233 Chain B； UniProt 77–233 Chain C； UniProt 77–233	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
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 77–233 Chain E； UniProt 77–233 Chain F； UniProt 77–233	Not recorded	No other associated polymer	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

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 6X85	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 mutation/modification 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 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 oligomeric state 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 oligomeric state 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 mutation/modification 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 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 mutation/modification 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 mutation/modification 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 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 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 oligomeric state 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 oligomeric state 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
3IT8 Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein Deposited 2009-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 82–233（152 aa） Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233 Chain B 82–233（152 aa） Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233 Chain C 82–233（152 aa） Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233	Not recorded	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
3IT8 Crystal structure of TNF alpha complexed with a poxvirus MHC-related TNF binding protein Deposited 2009-08-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 82–233（152 aa） Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233 Chain H 82–233（152 aa） Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233 Chain I 82–233（152 aa） Fragment：Tumor necrosis factor, soluble form, UNP residues 82-233	Not recorded	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
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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 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 mutation/modification 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 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 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 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 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 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 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
6X86 Crystal Structure of TNFalpha with indolinone compound 11 Deposited 2020-06-01	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 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 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 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 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 mutation/modification 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 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 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 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 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 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 2–158； UniProt 77–233 Author chain B； PDBConstruct 2–158； UniProt 77–233 Author chain C； PDBConstruct 2–158； UniProt 77–233 Author chain D； PDBConstruct 2–158； UniProt 77–233 Author chain E； PDBConstruct 2–158； UniProt 77–233 Author chain F； PDBConstruct 2–158； UniProt 77–233

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6x85
Deposition date deposition_date	2020-06-01
Structure title title	Crystal Structure of TNFalpha with indolinone compound 9
Keywords keywords	Trimer, inhibitor complex, CYTOKINE; CYTOKINE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.22 Å
Radius of gyration Rg (electron density) rg_electron	30.17 Å
Forward intensity I(0) i0	130398000.00
Molecular weight molecular_weight	93323.0 kDa
Excluded volume excluded_volume	118020 Å³
Envelope volume envelope_volume	145870 Å³
Hydration-shell volume shell_volume	40002 Å³
Envelope diameter envelope_diameter	102.2 Å
Shell Rg shell_rg	37.64 Å
Envelope Rg envelope_rg	30.22 Å
Shape Rg shape_rg	30.14 Å
Total Rg total_rg	30.94 Å
Total atoms total_atoms	6599
Residues n_residues	842
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	99.8 Å
Rg (real space) rg_real	31.23 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.3040e+08
I(0) uncertainty (real space) i0_real_error	2.1400e+06
Rg (reciprocal space) rg_reciprocal	31.23 Å
I(0) (reciprocal space) i0_reciprocal	130400000.0000
Solution quality estimate total_estimate	0.8861
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.363
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45070000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.872

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6x85a_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6x85b_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6x85c_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6x85d_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6x85e_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d6x85f_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

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8. Citations (1)

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Unit-cell length a length_a	252.508 Å
Unit-cell length b length_b	65.672 Å
Unit-cell length c length_c	54.241 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	29.110 Å
R factor r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2520

Description description	Tumor necrosis factor
Molecular weight formula_weight	17501.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6599

Crystal Structure of TNFalpha with indolinone compound 9

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tumor necrosis factor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	1-{[2-(difluoromethoxy)phenyl]methyl}-2,2-dimethyl-1,2-dihydro-3H-indol-3-one
Molecular weight formula_weight	317.3 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/x8/6x85/6x85.fit
pddf	/app/data/pr_computation/x8/6x85/6x85.pr.out
profile	/app/data/saxs_computation/x8/6x85/6x85.dat