MolNFT v1 · #82606 · protein
Crystal structure of type III pks arsc mutant
3VS9 · Type III polyketide synthase: “Crystal structure of type III pks arsc mutant”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.85). MolNFT v1 #82606 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VS9
- Type
- protein
- Length
- 3,176 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III polyketide synthase
- EC
- 2.3.1.74
- Ligands
- NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Type III polyketide synthase (EC 2.3.1.74) | protein | 401 | 45% helix, 22% strand | — |
| B | Type III polyketide synthase (EC 2.3.1.74) | protein | 397 | 44% helix, 22% strand | — |
| C | Type III polyketide synthase (EC 2.3.1.74) | protein | 396 | 44% helix, 21% strand | — |
| D | Type III polyketide synthase (EC 2.3.1.74) | protein | 401 | 44% helix, 22% strand | — |
| E | Type III polyketide synthase (EC 2.3.1.74) | protein | 400 | 45% helix, 22% strand | — |
| G | Type III polyketide synthase (EC 2.3.1.74) | protein | 397 | 44% helix, 23% strand | — |
| H | Type III polyketide synthase (EC 2.3.1.74) | protein | 383 | 43% helix, 23% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, C, B, H, D, E, F, G
- PG4 · Tetraethylene glycol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.85 | 0.97 | 45 | PG4 |
| 2 | 1030 | 0.83 | 0.84 | 104 | empty |
| 3 | 174 | 0.82 | 0.97 | 31 | PG4 |
| 4 | 986 | 0.82 | 0.83 | 109 | empty |
| 5 | 174 | 0.81 | 0.96 | 29 | PG4 |
Interfaces
12 interfaces between chains.
- B–H · 2739 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 2730 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2699 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2659 Ų buried · 35 hydrogen bonds · protein-protein
- B–F · 428 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VS9 · Crystal structure of type III PKS ArsC mutant · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 3VS9 · PDBe 3VS9
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