MolNFT v1 · #152983 · protein
Crystal structure of DNA polymerase sliding clamp from caulobacter crescentus
6IZO · Beta sliding clamp: “Crystal structure of DNA polymerase sliding clamp from caulobacter crescentus”. X-ray diffraction, 5 pockets (best druggability 0.38). MolNFT v1 #152983 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6IZO
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp
- UniProt
- P0CAU5
- Pockets
- 5 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 370 | 22% helix, 43% strand | P0CAU5 |
| B | Beta sliding clamp | protein | 371 | 22% helix, 43% strand | P0CAU5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.38 | 0.75 | 22 | empty |
| 2 | 70 | 0.32 | 0.75 | 17 | empty |
| 3 | 76 | 0.32 | 0.74 | 19 | empty |
| 4 | 65 | 0.31 | 0.75 | 17 | empty |
| 5 | 61 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6IZO · Crystal structure of DNA polymerase sliding clamp from Caulobacter crescentus · the same entry in another collection · chain A against A, TM-score 1.00
- P0CAU5 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0CAU5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0CAU5
- Elsewhere: RCSB PDB 6IZO · PDBe 6IZO · UniProt P0CAU5
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