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Crystal structure of the human tumor necrosis factor in complex with golimumab fv
Analyse Crystal structure of the human tumor necrosis factor in complex with golimumab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YOY
- Type
- protein
- Length
- 2,324 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; Golimumab light chain variable region; Golimumab heavy chain…
- UniProt
- P01375
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tumor necrosis factor | protein | 154 | 4% helix, 48% strand | P01375 |
| D, E, F, M, N, O | Golimumab light chain variable region | protein | 108 | 3% helix, 48% strand | — |
| G, H, P, Q, R | Golimumab heavy chain variable region | protein | 126 | 5% helix, 49% strand | — |
| I | Golimumab heavy chain variable region | protein | 125 | 5% helix, 51% strand | — |
| J, K, L | Tumor necrosis factor | protein | 153 | 4% helix, 50% strand | P01375 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.80 | 0.93 | 36 | empty |
| 2 | 754 | 0.80 | 0.84 | 55 | empty |
| 3 | 729 | 0.79 | 0.83 | 55 | empty |
| 4 | 80 | 0.76 | 0.98 | 20 | empty |
| 5 | 74 | 0.75 | 0.98 | 18 | empty |
Interfaces
30 interfaces between chains.
- J–K · 1214 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1187 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 1187 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1175 Ų buried · 12 hydrogen bonds · protein-protein
- J–L · 1154 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5YOY · Crystal structure of the human tumor necrosis factor in complex with golimumab Fv · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01375
- Elsewhere: RCSB PDB 5YOY · PDBe 5YOY · UniProt P01375
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