MolNFT v1 · #182822 · protein
PCNA from thermococcus gammatolerans: crystal III, collection 1, 2.00 a, 1.91 mgy
7N5M · DNA polymerase sliding clamp: “PCNA from thermococcus gammatolerans: crystal III, collection 1, 2.00 a, 1.91 mgy”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.68). MolNFT v1 #182822 on GenesisL1: 3D structure…
- PDB
- 7N5M
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase sliding clamp
- UniProt
- C5A5N6
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase sliding clamp | protein | 248 | 17% helix, 48% strand | C5A5N6 |
| B | DNA polymerase sliding clamp | protein | 247 | 17% helix, 46% strand | C5A5N6 |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.68 | 0.76 | 76 | GOL, SO4 |
| 2 | 195 | 0.48 | 0.76 | 28 | empty |
| 3 | 124 | 0.47 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7N5M · PCNA from Thermococcus gammatolerans: crystal III, collection 1, 2.00 A, 1.91 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 B 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 7N5M · PDBe 7N5M · UniProt C5A5N6
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