MolNFT v1 · #169313 · protein
Crystal structure of tnfalpha with fragment compound 6
6X83 · Tumor necrosis factor: “Crystal structure of tnfalpha with fragment compound 6”. X-ray diffraction, 1 ligand (UTS), 10 pockets (best druggability 0.86). MolNFT v1 #169313 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6X83
- Type
- protein
- Length
- 809 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor
- UniProt
- P01375
- Ligands
- UTS
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 1% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor | protein | 141 | 4% helix, 53% strand | P01375 |
| B | Tumor necrosis factor | protein | 138 | 2% helix, 50% strand | P01375 |
| C | Tumor necrosis factor | protein | 135 | 0% helix, 55% strand | P01375 |
| D | Tumor necrosis factor | protein | 127 | 0% helix, 55% strand | P01375 |
| E | Tumor necrosis factor | protein | 130 | 0% helix, 55% strand | P01375 |
| F | Tumor necrosis factor | protein | 138 | 2% helix, 52% strand | P01375 |
Ligands and binding sites
- UTS · 1-benzyl-1H-benzimidazole · ligand · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.86 | 0.88 | 105 | empty |
| 2 | 281 | 0.86 | 0.96 | 38 | UTS |
| 3 | 376 | 0.84 | 0.93 | 47 | UTS |
| 4 | 382 | 0.69 | 0.82 | 43 | empty |
| 5 | 79 | 0.46 | 0.81 | 18 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1105 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1099 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1035 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 912 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 480 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6X83 · Crystal Structure of TNFalpha with fragment compound 6 · 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 6X83 · PDBe 6X83 · UniProt P01375
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