MolNFT v1 · #104700 · protein
Crystal structure of type II menb from mycobacteria tuberculosis
4QII · 1,4-dihydroxy-2-naphthoyl-CoA synthase: “Crystal structure of type II menb from mycobacteria tuberculosis”. X-ray diffraction, 1 ligand (2NE), 20 pockets (best druggability 0.87). MolNFT v1 #104700 on GenesisL1: 3D structure…
- PDB
- 4QII
- Type
- protein
- Length
- 3,593 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
- 2NE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 44% 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 | 300 | 44% helix, 18% strand | P9WNP5 |
| B, C, G, H, I | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 301 | 44% helix, 18% strand | P9WNP5 |
| D | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 299 | 44% helix, 18% strand | P9WNP5 |
| E, F, K, L | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 298 | 44% helix, 18% strand | P9WNP5 |
| J | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 297 | 45% helix, 19% strand | P9WNP5 |
Ligands and binding sites
- 2NE · Salicylyl CoA · ligand · 12 copies · chains A, F, G, B, E, I, C, D, H, L, K, J
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, 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 | 424 | 0.87 | 0.95 | 63 | empty |
| 2 | 423 | 0.86 | 0.94 | 71 | empty |
| 3 | 379 | 0.80 | 0.89 | 52 | empty |
| 4 | 386 | 0.79 | 0.88 | 51 | empty |
| 5 | 426 | 0.79 | 0.87 | 56 | empty |
Interfaces
27 interfaces between chains.
- H–K · 2459 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 2456 Ų buried · 37 hydrogen bonds · protein-protein
- G–L · 2452 Ų buried · 36 hydrogen bonds · protein-protein
- I–J · 2450 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2445 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4QII · Crystal Structure of type II MenB from Mycobacteria tuberculosis · 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 4QII · PDBe 4QII · UniProt P9WNP5
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