MolNFT v1 · #79606 · protein
Crystal structure of escherichia COLI menb in complex with substrate analogue, osb-ncoa
3T88 · 1,4-dihydroxy-2-naphthoyl-CoA synthase: “Crystal structure of escherichia COLI menb in complex with substrate analogue, osb-ncoa”. X-ray diffraction, 2 ligands (S0N, CL), 20 pockets (best druggability 0.88). MolNFT v1 #79606 on…
- PDB
- 3T88
- Type
- protein
- Length
- 1,686 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
- S0N, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 281 | 46% helix, 19% strand | P0ABU0 |
Ligands and binding sites
- S0N · o-succinylbenzoyl-N-coenzyme A · ligand · 6 copies · chains A, E, B, F, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 6 copies · chains A, E, B, F, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C, B, D, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.88 | 0.95 | 48 | empty |
| 2 | 648 | 0.77 | 0.83 | 62 | PGE |
| 3 | 637 | 0.77 | 0.83 | 62 | PGE |
| 4 | 664 | 0.76 | 0.82 | 56 | PGE |
| 5 | 364 | 0.74 | 0.85 | 54 | S0N, CL |
Interfaces
12 interfaces between chains.
- A–E · 2579 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 2572 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2486 Ų buried · 38 hydrogen bonds · protein-protein
- C–F · 1630 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1625 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3T88 · Crystal structure of Escherichia coli MenB in complex with substrate analogue, OSB-NCoA · the same entry in another collection · chain C against C, 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 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 P0ABU0
- Elsewhere: RCSB PDB 3T88 · PDBe 3T88 · UniProt P0ABU0
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