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Crystal structure of menb from mycobacteria tuberculosis in complex with 1-hna-CoA
Analyse Crystal structure of menb from mycobacteria tuberculosis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QIJ
- Type
- protein
- Length
- 3,592 residues
- Chains
- 12
- 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
- P9WNP5
- Ligands
- 1HA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, J, K, L | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 301 | 45% helix, 18% strand | P9WNP5 |
| D, G | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 297 | 45% helix, 19% strand | P9WNP5 |
| E, F, H, I | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 298 | 45% helix, 18% strand | P9WNP5 |
Ligands and binding sites
- 1HA · 1-hydroxy-2-naphthoyl-CoA · ligand · 12 copies · chains A, F, B, E, C, D, G, K, H, J, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.87 | 0.88 | 136 | empty |
| 2 | 1099 | 0.85 | 0.86 | 130 | empty |
| 3 | 383 | 0.79 | 0.89 | 56 | empty |
| 4 | 397 | 0.79 | 0.88 | 52 | empty |
| 5 | 394 | 0.78 | 0.87 | 51 | empty |
Interfaces
26 interfaces between chains.
- C–D · 2481 Ų buried · 38 hydrogen bonds · protein-protein
- H–J · 2478 Ų buried · 38 hydrogen bonds · protein-protein
- I–L · 2473 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 2467 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2467 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4QIJ · Crystal structure of MenB from Mycobacteria tuberculosis in complex with 1-HNA-CoA · the same entry in another collection · chain L against L, 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 P9WNP5
- Elsewhere: RCSB PDB 4QIJ · PDBe 4QIJ · UniProt P9WNP5
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