MolNFT v1 · #126420 · protein
Structure of human tumor necrosis factor (TNF) in complex with the llama VHH1
5M2I: “Structure of human tumor necrosis factor (TNF) in complex with the llama VHH1”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #126420 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M2I
- Type
- protein
- Length
- 1,612 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; VHH1
- UniProt
- P01375
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Tumor necrosis factor | protein | 148 | 2% helix, 52% strand | P01375 |
| E | Tumor necrosis factor | protein | 146 | 2% helix, 53% strand | P01375 |
| G, H, I, J, K, L | VHH1 | protein | 121 | 10% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.74 | 0.85 | 56 | empty |
| 2 | 387 | 0.73 | 0.84 | 43 | empty |
| 3 | 54 | 0.72 | 0.99 | 16 | empty |
| 4 | 59 | 0.72 | 0.98 | 19 | empty |
| 5 | 344 | 0.60 | 0.77 | 36 | empty |
Interfaces
20 interfaces between chains.
- D–F · 1176 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1166 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1105 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1070 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5M2I · Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1 · 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 5M2I · PDBe 5M2I · UniProt P01375
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