Research workbench
Crystal structure of the RNA polymerase domain (rpd) of mycobacterium tuberculosis primase dnag in complex with a double-stranded DNA oligomer with a 6-nucleotide overhang
Analyse Crystal structure of the RNA polymerase domain (rpd) of mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W36
- Type
- protein + DNA
- Length
- 645 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase; Synthetic DNA 5'-tatcgtcccgcctc
- EC
- 2.7.7.-
- UniProt
- P9WNW1
- Ligands
- SR
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase (EC 2.7.7.-) | protein | 321 | 46% helix, 17% strand | P9WNW1 |
| B | DNA primase (EC 2.7.7.-) | protein | 322 | 46% helix, 17% strand | P9WNW1 |
| G | Synthetic DNA 5'-tatcgtcccgcctc | dna | 2 | — | — |
Ligands and binding sites
- SR · Strontium ion · metal · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.71 | 0.77 | 65 | empty |
| 2 | 299 | 0.57 | 0.77 | 39 | empty |
| 3 | 250 | 0.57 | 0.78 | 29 | empty |
| 4 | 138 | 0.50 | 0.79 | 21 | empty |
| 5 | 75 | 0.35 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 762 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 289 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 5W36 · Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WNW1 · AlphaFold monomer V2.0 prediction for DNA primase (P9WNW1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WNW1
- Elsewhere: RCSB PDB 5W36 · PDBe 5W36 · UniProt P9WNW1
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