MolNFT v1 · #94719 · protein
Scmenb im complex with 1-hydroxy-2-naphthoyl-CoA
4I52 · Naphthoate synthase: “Scmenb im complex with 1-hydroxy-2-naphthoyl-CoA”. X-ray diffraction, 2 ligands (1HA, CL), 20 pockets (best druggability 0.89). MolNFT v1 #94719 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I52
- Type
- protein
- Length
- 2,472 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naphthoate synthase
- EC
- 4.1.3.36
- UniProt
- P73495
- Ligands
- 1HA, CL
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, G, H, I | Naphthoate synthase (EC 4.1.3.36) | protein | 275 | 47% helix, 20% strand | P73495 |
| C, E, F | Naphthoate synthase (EC 4.1.3.36) | protein | 274 | 46% helix, 21% strand | P73495 |
Ligands and binding sites
- 1HA · 1-hydroxy-2-naphthoyl-CoA · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.89 | 0.91 | 169 | empty |
| 2 | 439 | 0.71 | 0.82 | 60 | empty |
| 3 | 325 | 0.64 | 0.80 | 46 | 1HA, CL |
| 4 | 409 | 0.64 | 0.78 | 61 | 1HA, CL |
| 5 | 321 | 0.64 | 0.80 | 46 | 1HA, CL |
Interfaces
14 interfaces between chains.
- G–I · 1393 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1386 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1378 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 1334 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1332 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4I52 · scMenB im complex with 1-hydroxy-2-naphthoyl-CoA · the same entry in another collection · chain D against D, 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 P73495
- Elsewhere: RCSB PDB 4I52 · PDBe 4I52 · UniProt P73495
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