Research workbench
Crystal structure of the catalytic domain of rpfb from mycobacterium tuberculosis in complex with trinag
Analyse Crystal structure of the catalytic domain of rpfb from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KPM
- Type
- protein
- Length
- 320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Resuscitation-promoting factor rpfb
- EC
- 3.-.-.-
- UniProt
- O05594
- Ligands
- BEN, NAG, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Resuscitation-promoting factor rpfb (EC 3.-.-.-) | protein | 80 | 55% helix, 3% strand | O05594 |
Ligands and binding sites
- BEN · Benzamidine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.62 | 0.80 | 34 | NAG, BEN |
| 2 | 215 | 0.48 | 0.75 | 31 | empty |
| 3 | 114 | 0.42 | 0.77 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 384 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 227 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 218 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4KPM · Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in… · 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 O05594
- Elsewhere: RCSB PDB 4KPM · PDBe 4KPM · UniProt O05594
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