MolNFT v1 · #140864 · protein
Crystal structure of the human tumor necrosis factor in complex with golimumab fv
5YOY: “Crystal structure of the human tumor necrosis factor in complex with golimumab fv”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #140864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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