MolNFT v1 · #166456 · protein + DNA
Crystal structure of Q38A human DNA polymerase eta bound with 8- oxoadenine (oxoa) and non-hydrolyzable dgtp analog (dgtp*)
6UQI: “Crystal structure of Q38A human DNA polymerase eta bound with 8- oxoadenine (oxoa) and non-hydrolyzable dgtp…”. X-ray diffraction, 2 ligands (XG4, MN), 6 pockets (best druggability 0.81). MolNFT v1 #166456 on GenesisL1: 3D…
- PDB
- 6UQI
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*(A38)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, MN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 43% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*(A38)P*AP*TP*GP*AP*CP*GP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.81 | 0.82 | 72 | XG4, MN |
| 2 | 521 | 0.71 | 0.81 | 49 | empty |
| 3 | 193 | 0.66 | 0.85 | 21 | empty |
| 4 | 93 | 0.44 | 0.79 | 19 | empty |
| 5 | 85 | 0.39 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1096 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–P · 645 Ų buried · 17 hydrogen bonds · protein-nucleic
- T–P · 375 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6UQI · Crystal structure of Q38A human DNA polymerase eta bound with 8-oxoadenine (oxoA) and… · 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 6UQI · PDBe 6UQI · UniProt Q9Y253
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