Research workbench
Cryo-EM MAP of DNA polymerase D from pyrococcus abyssi in complex with DNA
Analyse Cryo-EM MAP of DNA polymerase D from pyrococcus abyssi in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HMS
- Type
- protein + DNA
- Length
- 1,532 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase II small subunit; DNA polymerase II large SUBUNIT,DNA polymerase II large…
- EC
- 2.7.7.7, 3.1.11.1
- UniProt
- Q9V2F3, Q9V2F4
- Ligands
- ZN, FE
- Pockets
- 3 · best druggability 0.37
Structure
electron microscopy · 4 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase II small subunit (EC 2.7.7.7, 3.1.11.1) | protein | 400 | 0% helix, 0% strand | Q9V2F3 |
| B | DNA polymerase II large SUBUNIT,DNA polymerase II large subunit (EC 2.7.7.7, 3.1.11.1) | protein | 1101 | 0% helix, 0% strand | Q9V2F4 |
| P | DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)- 3') | dna | 15 | — | — |
| T | DNA (5'- D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.37 | 0.73 | 34 | empty |
| 2 | 111 | 0.33 | 0.73 | 20 | empty |
| 3 | 62 | 0.30 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- P–T · 712 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- B–T · 106 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–B · 102 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6HMS · Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V2F3 · AlphaFold monomer V2.0 prediction for DNA polymerase II small subunit (Q9V2F3) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9V2F4 · AlphaFold monomer V2.0 prediction for DNA polymerase II large subunit (Q9V2F4) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9V2F3
- Every structure of UniProt Q9V2F4
- Elsewhere: RCSB PDB 6HMS · PDBe 6HMS · UniProt Q9V2F3 · UniProt Q9V2F4
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