Research workbench
Crystal structure of mycobacterium tuberculosis RNase pH, the mycobacterium tuberculosis structural genomics consortium target RV1340
Analyse Crystal structure of mycobacterium tuberculosis RNase pH, the mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B4T
- Type
- protein
- Length
- 1,442 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pH
- EC
- 2.7.7.56
- UniProt
- Q10628
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease pH (EC 2.7.7.56) | protein | 243 | 32% helix, 30% strand | Q10628 |
| B, D | Ribonuclease pH (EC 2.7.7.56) | protein | 239 | 30% helix, 30% strand | Q10628 |
| C | Ribonuclease pH (EC 2.7.7.56) | protein | 241 | 32% helix, 30% strand | Q10628 |
| E, F | Ribonuclease pH (EC 2.7.7.56) | protein | 240 | 32% helix, 29% strand | Q10628 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.71 | 0.82 | 57 | PO4 |
| 2 | 690 | 0.70 | 0.77 | 81 | PO4 |
| 3 | 160 | 0.66 | 0.87 | 27 | empty |
| 4 | 345 | 0.65 | 0.80 | 57 | PO4 |
| 5 | 406 | 0.61 | 0.77 | 54 | PO4 |
Interfaces
11 interfaces between chains.
- C–D · 1535 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1476 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1460 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 1460 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1435 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3B4T · Crystal structure of Mycobacterium tuberculosis RNase PH, the Mycobacterium tuberculosis… · the same entry in another collection · chain D against D, 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 Q10628
- Elsewhere: RCSB PDB 3B4T · PDBe 3B4T · UniProt Q10628
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