Research workbench
Structure of human tumor necrosis factor (TNF) in complex with the llama VHH1
Analyse Structure of human tumor necrosis factor (TNF) in complex with the llama VHH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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