MolNFT v1 · #92321 · protein
Crystal structure of TNF-alpha in complex with infliximab Fab fragment
4G3Y · Infliximab Fab L: “Crystal structure of TNF-alpha in complex with infliximab Fab fragment”. X-ray diffraction, 7 pockets (best druggability 0.58). MolNFT v1 #92321 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4G3Y
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Infliximab Fab L; Infliximab Fab H; Tumor necrosis factor
- UniProt
- P01375
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Infliximab Fab L | protein | 214 | 6% helix, 50% strand | — |
| H | Infliximab Fab H | protein | 220 | 8% helix, 51% strand | — |
| C | Tumor necrosis factor | protein | 148 | 2% helix, 50% strand | P01375 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.58 | 0.73 | 56 | empty |
| 2 | 371 | 0.56 | 0.75 | 49 | empty |
| 3 | 191 | 0.50 | 0.77 | 24 | empty |
| 4 | 72 | 0.49 | 0.84 | 22 | empty |
| 5 | 183 | 0.46 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1700 Ų buried · 13 hydrogen bonds · protein-protein
- H–C · 616 Ų buried · 6 hydrogen bonds · protein-protein
- L–C · 477 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4G3Y · Crystal structure of TNF-alpha in complex with Infliximab Fab fragment · the same entry in another collection · chain L against L, 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 4G3Y · PDBe 4G3Y · UniProt P01375
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