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 1-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
- 5W35
- Type
- protein + DNA
- Length
- 649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA primase; Synthetic DNA oligomer 5'-ccacttccggtc; Synthetic DNA oligomer…
- EC
- 2.7.7.-
- UniProt
- P9WNW1
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% 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, 16% strand | P9WNW1 |
| C | Synthetic DNA oligomer 5'-ccacttccggtc | dna | 2 | — | — |
| D | Synthetic DNA oligomer 5'-tgaccggaagtgg | dna | 4 | — | — |
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 | 846 | 0.71 | 0.76 | 71 | empty |
| 2 | 290 | 0.56 | 0.76 | 37 | empty |
| 3 | 236 | 0.55 | 0.77 | 28 | empty |
| 4 | 128 | 0.48 | 0.79 | 20 | empty |
| 5 | 77 | 0.35 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 705 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–D · 11 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 5W35 · 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 5W35 · PDBe 5W35 · UniProt P9WNW1
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