Research workbench
Structure of E. COLI. 1,4-dihydroxy-2- naphthoyl coenzyme a synthases (menb) in complex with bicarbonate
Analyse Structure of E. COLI. 1,4-dihydroxy-2- naphthoyl coenzyme a synthases (menb) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ELS
- Type
- protein
- Length
- 1,571 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
- Ligands
- BCT, CL
- 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 | 267 | 46% helix, 18% strand | P0ABU0 |
| B | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 268 | 46% helix, 18% strand | P0ABU0 |
| C | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 241 | 47% helix, 19% strand | P0ABU0 |
| D | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 265 | 46% helix, 18% strand | P0ABU0 |
| E | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 266 | 46% helix, 18% 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
- BCT · Bicarbonate ion · ligand · 9 copies · chains A, B, E, C, D, F
- CL · Chloride ion · ion · 5 copies · chains A, C, D, B
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, D, F
- PEG · Di(hydroxyethyl)ether · additive · chains B, E, F
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 | 501 | 0.88 | 0.95 | 48 | EDO, CL |
| 2 | 662 | 0.76 | 0.82 | 74 | BCT |
| 3 | 648 | 0.74 | 0.80 | 65 | empty |
| 4 | 491 | 0.72 | 0.81 | 45 | empty |
| 5 | 469 | 0.70 | 0.81 | 62 | BCT, PEG |
Interfaces
12 interfaces between chains.
- B–D · 1783 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1773 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 1648 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1618 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1597 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4ELS · Structure of E. Coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex… · 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 C 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 4ELS · PDBe 4ELS · UniProt P0ABU0
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