Research workbench
Yeast DNA polymerase eta in complex with C8-2-acetylaminofluorene containing DNA
Analyse Yeast DNA polymerase eta in complex with C8-2-acetylaminofluorene containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XGP
- Type
- protein + DNA
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q04049
- Ligands
- CA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 510 | 40% helix, 19% strand | Q04049 |
| B | DNA polymerase eta (EC 2.7.7.7) | protein | 511 | 40% helix, 17% strand | Q04049 |
| P, Q | 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3' | dna | 9 | — | — |
| T | 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3' | dna | 11 | — | — |
| U | 5'-D(*CP*8FG*CP*TP*CP*AP*TP*CP*CP*AP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.82 | 0.84 | 60 | CA |
| 2 | 1047 | 0.79 | 0.81 | 79 | CA |
| 3 | 1101 | 0.79 | 0.80 | 98 | empty |
| 4 | 511 | 0.67 | 0.79 | 31 | empty |
| 5 | 494 | 0.61 | 0.75 | 33 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1360 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 738 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–U · 526 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 467 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- Q–U · 440 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2XGP · Yeast DNA polymerase eta in complex with C8-2-acetylaminofluorene containing DNA · the same entry in another collection · chain U against U, TM-score 1.00
- Q04049 · AlphaFold monomer V2.0 prediction for DNA polymerase eta (Q04049) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q04049
- Elsewhere: RCSB PDB 2XGP · PDBe 2XGP · UniProt Q04049
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