MolNFT v1 · #106268 · protein + DNA
Crystal structure of human DNA polymerase eta inserting dcmpnpp opposite a mefapy-dg adducted DNA template
4RU9: “Crystal structure of human DNA polymerase eta inserting dcmpnpp opposite a mefapy-dg adducted DNA template”. X-ray diffraction, 2 ligands (0KX, MG), 4 pockets (best druggability 0.82). MolNFT v1 #106268 on GenesisL1: 3D structure…
- PDB
- 4RU9
- Type
- protein + DNA
- Length
- 446 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; Nucleic acids template: CAT(MF7)ATGACGCT; Nucleic acids primar…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 0KX, MG
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 427 | 43% helix, 21% strand | Q9Y253 |
| T | Nucleic acids template: CAT(MF7)ATGACGCT | dna | 11 | — | — |
| P | Nucleic acids primar: agcgtcat | dna | 8 | — | — |
Ligands and binding sites
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.82 | 0.83 | 82 | 0KX, MG |
| 2 | 631 | 0.73 | 0.80 | 53 | empty |
| 3 | 94 | 0.42 | 0.78 | 19 | empty |
| 4 | 83 | 0.36 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1077 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 542 Ų buried · 11 hydrogen bonds · protein-nucleic
- T–P · 376 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4RU9 · Crystal structure of human DNA polymerase eta inserting dCMPNPP opposite a MeFapy-dG… · the same entry in another collection · 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 Q9Y253
- Elsewhere: RCSB PDB 4RU9 · PDBe 4RU9 · UniProt Q9Y253
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