MolNFT v1 · #180248 · protein + DNA
DNA polymerase mu (K438D), 8-OXODGTP:CT reaction state ternary complex, 50 mm MN2+ (30MIN)
7KTM · DNA-directed DNA/RNA polymerase mu: “DNA polymerase mu (K438D), 8-OXODGTP:CT reaction state ternary complex, 50 mm MN2+ (30MIN)”. X-ray diffraction, 4 ligands (8OG, 8DG, PPV), 3 pockets (best druggability 0.76). MolNFT v1 #180248 on…
- PDB
- 7KTM
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA/RNA polymerase mu; DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- 8OG, 8DG, PPV, MN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA/RNA polymerase mu (EC 2.7.7.7) | protein | 327 | 51% helix, 15% strand | Q9NP87 |
| T | DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3') | dna | 9 | — | — |
| P | DNA (5'-D(*CP*GP*TP*AP*(8OG))-3') | dna | 4 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- 8OG · 8-oxo-2'-deoxy-guanosine-5'-monophosphate · ligand · chains A, T, P
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · chains A, T, P
- PPV · Pyrophosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 10 copies · chains A, T, D, P
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, P, T
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.76 | 0.78 | 62 | 8OG, MN, 8DG, PPV, EDO |
| 2 | 92 | 0.48 | 0.82 | 15 | empty |
| 3 | 50 | 0.40 | 0.82 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–T · 682 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 366 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 339 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 207 Ų buried · 12 hydrogen bonds · nucleic-nucleic
- T–D · 196 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 7KTM · DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (30min) · the same entry in another collection · chain T against T, TM-score 1.00
- Q9NP87 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9NP87) · a predicted model of the same protein · chain A 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 Q9NP87
- Elsewhere: RCSB PDB 7KTM · PDBe 7KTM · UniProt Q9NP87
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