MolNFT v1 · #182818 · protein
PCNA from thermococcus gammatolerans: crystal I, collection 1, 1.95 a, 5.22 mgy
7N5I · DNA polymerase sliding clamp: “PCNA from thermococcus gammatolerans: crystal I, collection 1, 1.95 a, 5.22 mgy”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.72). MolNFT v1 #182818 on GenesisL1: 3D structure…
- PDB
- 7N5I
- 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
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase sliding clamp | protein | 248 | 17% helix, 46% strand | C5A5N6 |
| B, C | DNA polymerase sliding clamp | protein | 247 | 17% helix, 47% 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.72 | 0.76 | 102 | GOL, SO4 |
| 2 | 422 | 0.65 | 0.78 | 54 | GOL |
| 3 | 244 | 0.52 | 0.75 | 34 | GOL, SO4 |
| 4 | 79 | 0.41 | 0.79 | 16 | empty |
| 5 | 85 | 0.36 | 0.75 | 20 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 699 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 593 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7N5I · PCNA from Thermococcus gammatolerans: crystal I, collection 1, 1.95 A, 5.22 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 7N5I · PDBe 7N5I · UniProt C5A5N6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.