MolNFT v1 · #153574 · protein
Crystal structure of C. crescentus beta sliding clamp with peg bound to putative beta-motif tethering region
6JIR: “Crystal structure of C. crescentus beta sliding clamp with peg bound to putative beta-motif tethering region”. X-ray diffraction, 8 pockets (best druggability 0.63). MolNFT v1 #153574 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6JIR
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp
- UniProt
- P0CAU5
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 376 | 21% helix, 42% strand | P0CAU5 |
| B | Beta sliding clamp | protein | 372 | 21% helix, 43% strand | P0CAU5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- P6G · Hexaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.63 | 0.75 | 44 | EDO |
| 2 | 167 | 0.48 | 0.77 | 29 | GOL |
| 3 | 105 | 0.47 | 0.79 | 19 | empty |
| 4 | 113 | 0.39 | 0.75 | 23 | P6G |
| 5 | 80 | 0.34 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6JIR · Crystal structure of C. crescentus beta sliding clamp with PEG bound to putative… · 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 6JIR · PDBe 6JIR · UniProt P0CAU5
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