Research workbench
DNA polymerase from M. tuberculosis
Analyse DNA polymerase from M. tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PU7
- Type
- protein + DNA
- Length
- 1,103 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit alpha; Template; Primer
- EC
- 2.7.7.7
- UniProt
- A0A045J099
- Ligands
- 82W, ZN
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 1070 | 48% helix, 13% strand | A0A045J099 |
| T | Template | dna | 19 | — | — |
| P | Primer | dna | 14 | — | — |
Ligands and binding sites
- 82W · [(1~{S},3~{R},4~{R},5~{R},6~{R},7~{S},8~{R},11~{S}, 13~{S},16~{S},17~{R},18~{E})-13-methoxy-5,17,19-trimethyl-6-oxidanyl-16-[(1~{R})-1-oxidanylethyl]-14-oxidanylidene-2,15-dioxatetracyclo[9.8.0.0^{1,7}.0^{3, 8}]nonadeca-9,18-dien-4-yl] 1~{H}-pyrrole-2-carboxylate · ligand · chains A, T, P
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.78 | 0.82 | 62 | empty |
| 2 | 924 | 0.76 | 0.79 | 70 | ZN |
| 3 | 667 | 0.76 | 0.82 | 72 | empty |
| 4 | 294 | 0.72 | 0.85 | 39 | 82W |
| 5 | 267 | 0.54 | 0.77 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1475 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 720 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–P · 620 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Compared structures
- 7PU7 · DNA polymerase from M. 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 A0A045J099
- Elsewhere: RCSB PDB 7PU7 · PDBe 7PU7 · UniProt A0A045J099
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