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The crystal structure of menb (RV0548C) from mycobacterium tuberculosis in complex with the CoA portion of naphthoyl CoA
Analyse The crystal structure of menb (RV0548C) from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RJN
- Type
- protein
- Length
- 779 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menb
- EC
- 4.1.3.36
- UniProt
- O06414
- Ligands
- COA, EP1
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Menb (EC 4.1.3.36) | protein | 259 | 46% helix, 19% strand | O06414 |
| B | Menb (EC 4.1.3.36) | protein | 275 | 44% helix, 17% strand | O06414 |
| C | Menb (EC 4.1.3.36) | protein | 245 | 46% helix, 20% strand | O06414 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains B
- EP1 · 3-[4-(2-hydroxyethyl)piperazin-1-yl]propane-1-sulfonic acid · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.68 | 0.84 | 43 | EP1 |
| 2 | 152 | 0.50 | 0.78 | 23 | empty |
| 3 | 235 | 0.48 | 0.74 | 32 | empty |
| 4 | 63 | 0.40 | 0.80 | 20 | empty |
| 5 | 71 | 0.40 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1485 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1257 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1244 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1RJN · The Crystal Structure of MenB (Rv0548c) from Mycobacterium tuberculosis in Complex with… · 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 1RJN · PDBe 1RJN · UniProt O06414
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