MolNFT v1 · #110981 · protein + DNA
Ternary complex of human DNA polymerase mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dumpnpp
4YD1 · DNA-directed DNA/RNA polymerase mu: “Ternary complex of human DNA polymerase mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable…”. X-ray diffraction, 4 ligands (DUP, MG, NA), 2 pockets (best druggability 0.78). MolNFT…
- PDB
- 4YD1
- Type
- protein + DNA
- Length
- 352 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*TP*AP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- DUP, MG, NA, CL
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA/RNA polymerase mu (EC 2.7.7.7) | protein | 334 | 50% helix, 16% strand | Q9NP87 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*G)-3') | dna | 10 | — | — |
| P | DNA (5'-D(*CP*GP*TP*A)-3') | dna | 4 | — | — |
| 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
- MG · Magnesium ion · metal · 3 copies · chains A, P, T
- NA · Sodium ion · metal · chains A, P
- CL · Chloride ion · ion · 4 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, P
- GOL · Glycerol · additive · 2 copies · chains A, T
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 | 1059 | 0.78 | 0.80 | 71 | MG, EDO, DUP, CL, NA |
| 2 | 127 | 0.44 | 0.77 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–T · 718 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–P · 399 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 365 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 202 Ų buried · 12 hydrogen bonds · nucleic-nucleic
- T–D · 194 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 4YD1 · Ternary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate and an incoming… · 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 4YD1 · PDBe 4YD1 · UniProt Q9NP87
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