MolNFT v1 · #168117 · protein + DNA
Crystal structure of human polymerase eta complexed with N7- benzylguanine and dctp*
6W5X · DNA polymerase eta: “Crystal structure of human polymerase eta complexed with N7- benzylguanine and dctp*”. X-ray diffraction, 2 ligands (0KX, MN), 7 pockets (best druggability 0.80). MolNFT v1 #168117 on GenesisL1: 3D structure…
- PDB
- 6W5X
- Type
- protein + DNA
- Length
- 446 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*(DRG)P*CP*TP*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 0KX, MN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 427 | 43% helix, 23% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*(DRG)P*CP*TP*CP*AP*CP*AP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-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
- MN · Manganese (II) 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.80 | 0.82 | 65 | 0KX, MN |
| 2 | 419 | 0.72 | 0.83 | 42 | empty |
| 3 | 202 | 0.68 | 0.86 | 22 | empty |
| 4 | 79 | 0.58 | 0.87 | 15 | empty |
| 5 | 138 | 0.51 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1047 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 589 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 386 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6W5X · Crystal structure of human polymerase eta complexed with N7-benzylguanine and dCTP* · 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 6W5X · PDBe 6W5X · UniProt Q9Y253
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