MolNFT v1 · #157241 · protein
Structure of the 6TH type III domain from human fibronectin
6MSV: “Structure of the 6TH type III domain from human fibronectin”. X-ray diffraction, 11 pockets (best druggability 0.85). MolNFT v1 #157241 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MSV
- Type
- protein
- Length
- 1,015 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibronectin
- UniProt
- P02751
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibronectin | protein | 86 | 0% helix, 52% strand | P02751 |
| B, G, J, L | Fibronectin | protein | 83 | 0% helix, 53% strand | P02751 |
| C | Fibronectin | protein | 85 | 0% helix, 51% strand | P02751 |
| D | Fibronectin | protein | 90 | 0% helix, 49% strand | P02751 |
| E, F, K | Fibronectin | protein | 84 | 0% helix, 52% strand | P02751 |
| H | Fibronectin | protein | 89 | 0% helix, 48% strand | P02751 |
| I | Fibronectin | protein | 81 | 0% helix, 56% strand | P02751 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, L, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.85 | 0.86 | 116 | empty |
| 2 | 270 | 0.69 | 0.85 | 44 | empty |
| 3 | 86 | 0.68 | 0.93 | 29 | empty |
| 4 | 676 | 0.66 | 0.75 | 58 | GOL |
| 5 | 134 | 0.66 | 0.89 | 24 | empty |
Interfaces
26 interfaces between chains.
- E–K · 792 Ų buried · 11 hydrogen bonds · protein-protein
- A–J · 754 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 752 Ų buried · 12 hydrogen bonds · protein-protein
- C–I · 743 Ų buried · 12 hydrogen bonds · protein-protein
- B–L · 733 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6MSV · Structure of the 6th type III domain from human fibronectin · 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 P02751
- Elsewhere: RCSB PDB 6MSV · PDBe 6MSV · UniProt P02751
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