MolNFT v1 · #168496 · protein + DNA
Nucleotide incorporation intermediate into quaternary complex of human polymerase mu on a complementary DNA double-strand break substrate
6WID · DNA-directed DNA/RNA polymerase mu: “Nucleotide incorporation intermediate into quaternary complex of human polymerase mu on a complementary DNA…”. X-ray diffraction, 5 ligands (DUP, PPV, MG), 2 pockets (best druggability 0.72).…
- PDB
- 6WID
- Type
- protein + DNA
- Length
- 348 residues
- Chains
- 5
- 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*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- DUP, PPV, MG, NA, CL
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 5 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 | 330 | 51% helix, 15% strand | Q9NP87 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*T)-3') | dna | 6 | — | — |
| U | DNA (5'-D(*AP*CP*G)-3') | dna | 3 | — | — |
| P | DNA (5'-D(*CP*GP*TP*AP*T)-3') | dna | 5 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
- PPV · Pyrophosphate · ligand · chains A, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · chains A, P
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · 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 | 1066 | 0.72 | 0.76 | 58 | PPV |
| 2 | 84 | 0.48 | 0.83 | 15 | empty |
Interfaces
8 interfaces between chains.
- A–P · 598 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–T · 425 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 372 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–U · 291 Ų buried · 6 hydrogen bonds · protein-nucleic
- T–D · 196 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6WID · Nucleotide incorporation intermediate into quaternary complex of human Polymerase Mu on a… · 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 6WID · PDBe 6WID · UniProt Q9NP87
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