Research workbench
Crystal structure of human DNA polymerase eta complexed with N7- nitrogen half-mustard guanine (nhmg) and dctp*
Analyse Crystal structure of human DNA polymerase eta complexed with N7- nitrogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V5K
- Type
- protein + DNA
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- QRV, 0KX, MN
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 427 | 44% helix, 22% strand | Q9Y253 |
| P | DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3') | dna | 8 | — | — |
| T | DNA (5'-D(*CP*AP*T*(QRV)P*CP*TP*CP*AP*CP*AP*CP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- QRV · 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7-{2-[(2-hydroxyethyl)(phenyl) amino]ethyl}-6-oxo-6,9-dihydro-1H-purin-7-ium · ligand · chains A, P, T
- 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains A, P
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.81 | 0.84 | 68 | QRV, 0KX, MN |
| 2 | 353 | 0.76 | 0.87 | 37 | empty |
| 3 | 219 | 0.64 | 0.83 | 27 | empty |
| 4 | 97 | 0.39 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 767 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 584 Ų buried · 15 hydrogen bonds · protein-nucleic
- P–T · 370 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6V5K · Crystal structure of human DNA polymerase eta complexed with N7-nitrogen half-mustard… · 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 6V5K · PDBe 6V5K · UniProt Q9Y253
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