Research workbench
PCNA from thermococcus gammatolerans: crystal II, collection 1, 1.98 a, 3.84 mgy
Analyse PCNA from thermococcus gammatolerans: crystal II, collection 1, 1.98 a, 3.84 mgy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N5K
- Type
- protein
- Length
- 990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp
- UniProt
- C5A5N6
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase sliding clamp | protein | 248 | 17% helix, 47% strand | C5A5N6 |
| B, C | DNA polymerase sliding clamp | protein | 247 | 17% helix, 46% strand | C5A5N6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
- GOL · Glycerol · additive · 18 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.72 | 0.76 | 103 | GOL, SO4 |
| 2 | 584 | 0.66 | 0.76 | 61 | GOL, SO4 |
| 3 | 128 | 0.47 | 0.78 | 18 | GOL |
| 4 | 124 | 0.46 | 0.78 | 21 | empty |
| 5 | 130 | 0.42 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 685 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 587 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 535 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7N5K · PCNA from Thermococcus gammatolerans: crystal II, collection 1, 1.98 A, 3.84 MGy · the same entry in another collection · chain A against A, TM-score 1.00
- C5A5N6 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp (C5A5N6) · 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 C5A5N6
- Elsewhere: RCSB PDB 7N5K · PDBe 7N5K · UniProt C5A5N6
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