Research workbench
Crystal structure of menb (RV0548C) from mycobacterium tuberculosis
Analyse Crystal structure of menb (RV0548C) from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RJM
- Type
- protein
- Length
- 717 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
- EP1
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Menb (EC 4.1.3.36) | protein | 239 | 47% helix, 19% strand | O06414 |
| B | Menb (EC 4.1.3.36) | protein | 240 | 47% helix, 20% strand | O06414 |
| C | Menb (EC 4.1.3.36) | protein | 238 | 44% helix, 20% strand | O06414 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.68 | 0.87 | 36 | EP1 |
| 2 | 53 | 0.45 | 0.84 | 17 | empty |
| 3 | 61 | 0.39 | 0.80 | 20 | empty |
| 4 | 97 | 0.38 | 0.75 | 13 | empty |
| 5 | 98 | 0.37 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1299 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1276 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1272 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1RJM · Crystal Structure of MenB (Rv0548c) from Mycobacterium tuberculosis · 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 1RJM · PDBe 1RJM · UniProt O06414
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