Research workbench
Crystal structure of the catalytic domain of rpfb from mycobacterium tuberculosis
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
- 4KL7
- 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
- SO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Resuscitation-promoting factor rpfb (EC 3.-.-.-) | protein | 80 | 55% helix, 5% strand | O05594 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.60 | 0.80 | 34 | empty |
| 2 | 226 | 0.51 | 0.76 | 36 | empty |
| 3 | 60 | 0.32 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 366 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 267 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 217 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 174 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4KL7 · Crystal structure of the catalytic domain of RpfB 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 O05594
- Elsewhere: RCSB PDB 4KL7 · PDBe 4KL7 · UniProt O05594
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