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 heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count | Chain A； UniProt 77–233 Chain B； UniProt 77–233 Chain C； UniProt 77–233 | Not recorded | Golimumab light chain variable region × 3 Golimumab heavy chain variable region × 3 | 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 |
| 2 | Protein heterocomplex Heteromer Protein × 9 PDB declaration: nonameric（9） Consistent with protein copy count | Chain J； UniProt 77–233 Chain K； UniProt 77–233 Chain L； UniProt 77–233 | Not recorded | Golimumab light chain variable region × 3 Golimumab heavy chain variable region × 3 | 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 |
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 5YOY | 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 |
| 6OOY Asymmetric hTNF-alpha Deposited 2019-04-23 | 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 9–165； UniProt 77–233 Author chain B； PDBConstruct 9–165； UniProt 77–233 Author chain C； PDBConstruct 9–165； UniProt 77–233 Author chain J； PDBConstruct 9–165； UniProt 77–233 Author chain K； PDBConstruct 9–165； UniProt 77–233 Author chain L； PDBConstruct 9–165； UniProt 77–233 |
