MolNFT v1 · #83275 · protein
Crystal structure of tnfalpha in complex with adalimumab Fab fragment
3WD5 · Tumor necrosis factor: “Crystal structure of tnfalpha in complex with adalimumab Fab fragment”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #83275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WD5
- Type
- protein
- Length
- 579 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; Adalimumab light chain; Adalimumab heavy chain
- UniProt
- P01375
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 152 | 4% helix, 48% strand | P01375 |
| L | Adalimumab light chain | protein | 213 | 6% helix, 46% strand | — |
| H | Adalimumab heavy chain | protein | 214 | 4% helix, 50% strand | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.65 | 0.75 | 64 | empty |
| 2 | 72 | 0.56 | 0.88 | 22 | empty |
| 3 | 138 | 0.50 | 0.79 | 30 | empty |
| 4 | 69 | 0.50 | 0.85 | 14 | empty |
| 5 | 140 | 0.44 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1724 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 614 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 321 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3WD5 · Crystal structure of TNFalpha in complex with Adalimumab Fab fragment · 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 3WD5 · PDBe 3WD5 · UniProt P01375
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