Research workbench
Binary complex of human DNA polymerase mu with MN8OXODGTP
Analyse Binary complex of human DNA polymerase mu with MN8OXODGTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IPK
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA/RNA polymerase mu
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- 8DG, MN, SO4
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA/RNA polymerase mu (EC 2.7.7.7) | protein | 329 | 51% helix, 16% strand | Q9NP87 |
Ligands and binding sites
- 8DG · 8-oxo-2'-deoxyguanosine-5'-triphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.59 | 0.73 | 58 | MN, 8DG, SO4 |
Compared structures
- 6IPK · Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NP87 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9NP87) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9NP87
- Elsewhere: RCSB PDB 6IPK · PDBe 6IPK · UniProt Q9NP87
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