Research workbench
Crystal structure of human polymerase eta complexed with syn N7- benzylguanine
Analyse Crystal structure of human polymerase eta complexed with syn N7- benzylguanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L69
- 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*(7BG)P*CP*TP*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Pockets
- 6 · best druggability 0.77
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 | 427 | 43% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*(7BG)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 | — | — |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.77 | 0.83 | 45 | empty |
| 2 | 497 | 0.72 | 0.82 | 47 | empty |
| 3 | 242 | 0.65 | 0.83 | 25 | empty |
| 4 | 261 | 0.52 | 0.76 | 32 | empty |
| 5 | 105 | 0.48 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1085 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–P · 609 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 393 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7L69 · Crystal structure of human polymerase eta complexed with syn N7-benzylguanine · 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 7L69 · PDBe 7L69 · UniProt Q9Y253
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