Research workbench
Crystal structure of escherichia COLI menb, the 1,4-dihydroxy-2- naphthoyl-CoA synthase in vitamin K2 biosynthesis
Analyse Crystal structure of escherichia COLI menb, the 1,4-dihydroxy-2- naphthoyl-CoA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T89
- Type
- protein
- Length
- 1,579 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,4-dihydroxy-2-naphthoyl-CoA synthase
- EC
- 4.1.3.36
- UniProt
- P0ABU0
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 270 | 45% helix, 17% strand | P0ABU0 |
| B | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 263 | 46% helix, 18% strand | P0ABU0 |
| C | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 246 | 46% helix, 18% strand | P0ABU0 |
| D | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 267 | 48% helix, 18% strand | P0ABU0 |
| E | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 269 | 47% helix, 17% strand | P0ABU0 |
| F | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 264 | 47% helix, 18% strand | P0ABU0 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, C, D, B, E, F
- MLI · Malonate ion · additive · 6 copies · chains A, F, B, D, C, E
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 | 492 | 0.88 | 0.95 | 48 | empty |
| 2 | 739 | 0.78 | 0.82 | 78 | empty |
| 3 | 502 | 0.75 | 0.83 | 66 | MLI |
| 4 | 451 | 0.72 | 0.82 | 46 | empty |
| 5 | 432 | 0.72 | 0.82 | 43 | empty |
Interfaces
12 interfaces between chains.
- C–E · 1739 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1702 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1687 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1660 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1571 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3T89 · Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in… · the same entry in another collection · chain F against F, TM-score 1.00
- P0ABU0 · AlphaFold monomer V2.0 prediction for 1,4-dihydroxy-2-naphthoyl-CoA synthase (P0ABU0) · a predicted model of the same protein · chain D 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 P0ABU0
- Elsewhere: RCSB PDB 3T89 · PDBe 3T89 · UniProt P0ABU0
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