MolNFT v1 · #110982 · protein + DNA
Nicked complex of human DNA polymerase mu with 2-nt gapped DNA substrate
4YD2 · DNA-directed DNA/RNA polymerase mu: “Nicked complex of human DNA polymerase mu with 2-nt gapped DNA substrate”. X-ray diffraction, 3 ligands (PPV, NA, CL), 3 pockets (best druggability 0.72). MolNFT v1 #110982 on GenesisL1: 3D…
- PDB
- 4YD2
- Type
- protein + DNA
- Length
- 339 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*AP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- PPV, NA, CL
- Pockets
- 3 · best druggability 0.72
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 | 323 | 51% helix, 15% strand | Q9NP87 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*AP*T)-3') | dna | 7 | — | — |
| 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
- PPV · Pyrophosphate · ligand · chains A, P
- NA · Sodium ion · metal · 3 copies · chains A, P
- CL · Chloride ion · ion · 3 copies · chains A, D
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 | 1035 | 0.72 | 0.76 | 53 | NA, PPV |
| 2 | 72 | 0.48 | 0.84 | 19 | empty |
| 3 | 116 | 0.41 | 0.77 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–P · 539 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–T · 457 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 370 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–D · 197 Ų buried · 17 hydrogen bonds · nucleic-nucleic
- T–P · 106 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 4YD2 · Nicked complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate · 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 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 Q9NP87
- Elsewhere: RCSB PDB 4YD2 · PDBe 4YD2 · UniProt Q9NP87
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