Research workbench
Cryo-EM structure of the DNA-bound pold-PCNA processive complex from P. abyssi
Analyse Cryo-EM structure of the DNA-bound pold-PCNA processive complex from P. abyssi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T8H
- Type
- protein + DNA
- Length
- 2,380 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp; DNA polymerase II small subunit; DP2 subunit of D-family…
- EC
- 2.7.7.7, 3.1.11.1
- UniProt
- Q9UYX8, Q9V2F3
- Ligands
- ZN, FE
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, C, D | DNA polymerase sliding clamp | protein | 246 | 19% helix, 46% strand | Q9UYX8 |
| A | DNA polymerase II small subunit (EC 2.7.7.7, 3.1.11.1) | protein | 420 | 23% helix, 28% strand | Q9V2F3 |
| B | DP2 subunit of D-family DNA-polymerase (EC 2.7.7.7) | protein | 1188 | 39% helix, 13% strand | — |
| P | DNA primer | dna | 17 | — | — |
| T | DNA template | dna | 17 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.81 | 0.84 | 99 | empty |
| 2 | 1148 | 0.76 | 0.78 | 81 | empty |
| 3 | 543 | 0.74 | 0.82 | 50 | empty |
| 4 | 54 | 0.73 | 0.98 | 18 | empty |
| 5 | 50 | 0.73 | 0.98 | 17 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2095 Ų buried · 18 hydrogen bonds · protein-protein
- P–T · 814 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- E–D · 706 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 9 hydrogen bonds · protein-protein
- E–C · 691 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6T8H · Cryo-EM structure of the DNA-bound PolD-PCNA processive complex from P. abyssi · the same entry in another collection · chain T against T, 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 1.00
- Q9UYX8 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp (Q9UYX8) · a predicted model of the same protein · chain E 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 Q9UYX8
- Every structure of UniProt Q9V2F3
- Elsewhere: RCSB PDB 6T8H · PDBe 6T8H · UniProt Q9UYX8 · UniProt Q9V2F3
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