MolNFT v1 · #137601 · protein
X-ray diffraction data of DNA polymerase eta (RAD30) of saccharomyces cerevisiae with a single magnesium bound in absence of DNA and incoming dntp
5VTP: “X-ray diffraction data of DNA polymerase eta (RAD30) of saccharomyces cerevisiae with a single magnesium…”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.49). MolNFT v1 #137601 on GenesisL1: 3D structure, binding…
- PDB
- 5VTP
- Type
- protein
- Length
- 510 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta
- EC
- 2.7.7.7
- UniProt
- Q04049
- Ligands
- MG
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 510 | 39% helix, 17% strand | Q04049 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.49 | 0.76 | 33 | MG |
| 2 | 65 | 0.40 | 0.80 | 17 | empty |
| 3 | 50 | 0.38 | 0.81 | 14 | empty |
| 4 | 76 | 0.34 | 0.75 | 14 | empty |
| 5 | 52 | 0.33 | 0.78 | 12 | empty |
Compared structures
- 5VTP · X-ray diffraction data of DNA Polymerase Eta (RAD30) of Saccharomyces cerevisiae with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04049 · AlphaFold monomer V2.0 prediction for DNA polymerase eta (Q04049) · a predicted model of the same protein · chain A 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 5VTP · PDBe 5VTP · UniProt Q04049
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