Research workbench
DNA polymerase mu, 8-OXORGTP:CT product state ternary complex, 50 mm MN2+ (2160 min)
Analyse DNA polymerase mu, 8-OXORGTP:CT product state ternary complex, 50 mm MN2+ (2160… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VFC
- Type
- protein + DNA
- Length
- 345 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*AP*TP*AP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- MN, NA, PO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 52% 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 | 52% helix, 15% strand | Q9NP87 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3') | dna | 9 | — | — |
| P | DNA (5'-D(*CP*GP*TP*AP*(8GM))-3') | dna | 5 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, P, D, T
- NA · Sodium ion · metal · chains A, P
- PO4 · Phosphate ion · ion · chains A, P
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, T, P
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
- 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.72 | 0.76 | 55 | MN, PO4, DTT |
| 2 | 108 | 0.49 | 0.81 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–T · 684 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 610 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 345 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 247 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- T–D · 194 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (additive adduct, nucleotide modification).
Compared structures
- 6VFC · DNA Polymerase Mu, 8-oxorGTP:Ct Product State Ternary Complex, 50 mM Mn2+ (2160 min) · the same entry in another collection · chain A against A, 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 6VFC · PDBe 6VFC · UniProt Q9NP87
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