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Crystal structure of human DNA polymerase eta in ternary complex with native DNA and incoming nucleotide (dcp)
Analyse Crystal structure of human DNA polymerase eta in ternary complex with native… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O3N
- 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*GP*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 0KX, MG
- Pockets
- 5 · best druggability 0.79
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*GP*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
- 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
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.79 | 0.81 | 65 | 0KX, MG |
| 2 | 547 | 0.73 | 0.81 | 48 | empty |
| 3 | 218 | 0.64 | 0.83 | 23 | empty |
| 4 | 94 | 0.46 | 0.80 | 19 | empty |
| 5 | 86 | 0.39 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1059 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 610 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 376 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 4O3N · Crystal structure of human dna polymerase eta in ternary complex with native dna 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 4O3N · PDBe 4O3N · UniProt Q9Y253
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