MolNFT v1 · #126424 · protein
Complex between human TNF alpha and llama VHH3
5M2M · Tumor necrosis factor: “Complex between human TNF alpha and llama VHH3”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #126424 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M2M
- Type
- protein
- Length
- 1,661 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; Llama nanobody VHH3
- UniProt
- P01375
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Tumor necrosis factor | protein | 150 | 2% helix, 49% strand | P01375 |
| B | Tumor necrosis factor | protein | 151 | 2% helix, 48% strand | P01375 |
| C, G | Tumor necrosis factor | protein | 150 | 2% helix, 49% strand | P01375 |
| D, E, F, H, J, N | Llama nanobody VHH3 | protein | 127 | 5% helix, 47% strand | — |
| M | Tumor necrosis factor | protein | 148 | 0% helix, 49% strand | P01375 |
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.76 | 0.83 | 59 | empty |
| 2 | 69 | 0.75 | 0.99 | 21 | empty |
| 3 | 659 | 0.75 | 0.81 | 56 | empty |
| 4 | 56 | 0.72 | 0.99 | 17 | empty |
| 5 | 88 | 0.57 | 0.86 | 29 | empty |
Interfaces
12 interfaces between chains.
- G–I · 1190 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1127 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1125 Ų buried · 13 hydrogen bonds · protein-protein
- I–M · 1086 Ų buried · 13 hydrogen bonds · protein-protein
- G–M · 1053 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5M2M · Complex between human TNF alpha and Llama VHH3 · 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 5M2M · PDBe 5M2M · UniProt P01375
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