MolNFT v1 · #79608 · protein
Crystal structure of mycobacterium tuberculosis menb in complex with substrate analogue, osb-ncoa
3T8A · 1,4-dihydroxy-2-naphthoyl-CoA synthase: “Crystal structure of mycobacterium tuberculosis menb in complex with substrate analogue, osb-ncoa”. X-ray diffraction, 1 ligand (S0N), 12 pockets (best druggability 0.76). MolNFT v1 #79608 on…
- PDB
- 3T8A
- Type
- protein
- Length
- 775 residues
- Chains
- 3
- 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
- O06414
- Ligands
- S0N
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 252 | 47% helix, 19% strand | O06414 |
| B | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 274 | 45% helix, 18% strand | O06414 |
| C | 1,4-dihydroxy-2-naphthoyl-CoA synthase (EC 4.1.3.36) | protein | 249 | 44% helix, 20% strand | O06414 |
Ligands and binding sites
- S0N · o-succinylbenzoyl-N-coenzyme A · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.76 | 0.83 | 59 | empty |
| 2 | 320 | 0.59 | 0.78 | 35 | empty |
| 3 | 177 | 0.46 | 0.75 | 24 | empty |
| 4 | 134 | 0.44 | 0.76 | 22 | empty |
| 5 | 73 | 0.39 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1311 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1233 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1164 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3T8A · Crystal structure of Mycobacterium tuberculosis MenB in complex with substrate analogue… · the same entry in another collection · 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 O06414
- Elsewhere: RCSB PDB 3T8A · PDBe 3T8A · UniProt O06414
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