MolNFT v1 · #90524 · protein
Structure of apo E.COLI. 1,4-dihydroxy-2- naphthoyl CoA synthases with cl
4ELX · 1,4-dihydroxy-2-naphthoyl-CoA synthase: “Structure of apo E.COLI. 1,4-dihydroxy-2- naphthoyl CoA synthases with cl”. X-ray diffraction, 2 ligands (CL, PO4), 16 pockets (best druggability 0.87). MolNFT v1 #90524 on GenesisL1: 3D…
- PDB
- 4ELX
- Type
- protein
- Length
- 1,574 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
- CL, PO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 268 | 46% helix, 17% strand | P0ABU0 |
| B | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 269 | 45% helix, 17% strand | P0ABU0 |
| C | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 242 | 49% helix, 19% strand | P0ABU0 |
| D | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 265 | 49% helix, 17% strand | P0ABU0 |
| E | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 266 | 48% helix, 17% strand | P0ABU0 |
| F | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 264 | 45% helix, 17% strand | P0ABU0 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 7 copies · chains A, C, B, E, D, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, E, F, A, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.87 | 0.94 | 48 | PEG, CL |
| 2 | 649 | 0.78 | 0.83 | 57 | empty |
| 3 | 773 | 0.78 | 0.82 | 81 | CL |
| 4 | 496 | 0.74 | 0.83 | 57 | CL |
| 5 | 599 | 0.73 | 0.81 | 68 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1792 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1741 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1627 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 1625 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1586 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4ELX · Structure of apo E.coli. 1,4-dihydroxy-2- naphthoyl CoA synthases with Cl · 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 F against A, TM-score 0.99
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 4ELX · PDBe 4ELX · UniProt P0ABU0
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