MolNFT v1 · #58469 · protein
Crystal structure of mycobacterium tuberculosis RNase pH, the mycobacterium tuberculosis structural genomics consortium target RV1340
3B4T · Ribonuclease pH: “Crystal structure of mycobacterium tuberculosis RNase pH, the mycobacterium tuberculosis structural genomics…”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.71). MolNFT v1 #58469 on GenesisL1…
- 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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