Research workbench
Synechocystis sp. pcc 6803 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase (menb) in complex with salicylyl-CoA
Analyse Synechocystis sp. pcc 6803 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase (menb)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I4Z
- Type
- protein
- Length
- 2,474 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
- 2NE, BCT
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H, I | Naphthoate synthase (EC 4.1.3.36) | protein | 275 | 46% helix, 20% strand | P73495 |
| B | Naphthoate synthase (EC 4.1.3.36) | protein | 274 | 46% helix, 21% strand | P73495 |
Ligands and binding sites
- 2NE · Salicylyl CoA · ligand · 9 copies · chains A, F, B, D, C, E, G, H, I
- BCT · Bicarbonate ion · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
- MLI · Malonate ion · additive · 2 copies · chains A, C, D, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.88 | 0.95 | 48 | empty |
| 2 | 680 | 0.83 | 0.87 | 61 | empty |
| 3 | 689 | 0.83 | 0.87 | 63 | empty |
| 4 | 624 | 0.83 | 0.88 | 68 | empty |
| 5 | 404 | 0.74 | 0.84 | 59 | empty |
Interfaces
17 interfaces between chains.
- C–E · 2476 Ų buried · 45 hydrogen bonds · protein-protein
- A–F · 2464 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 2420 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 1776 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1771 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4I4Z · Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in… · 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 P73495
- Elsewhere: RCSB PDB 4I4Z · PDBe 4I4Z · UniProt P73495
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