MolNFT v1 · #99973 · protein
E. COLI sliding clamp in complex with (S)-carprofen
4MJR · DNA polymerase III subunit beta: “E. COLI sliding clamp in complex with (S)-carprofen”. X-ray diffraction, 3 ligands (0LA, CA, CL), 6 pockets (best druggability 0.43). MolNFT v1 #99973 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4MJR
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta
- EC
- 2.7.7.7
- UniProt
- P0A988
- Ligands
- 0LA, CA, CL
- Pockets
- 6 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 360 | 23% helix, 48% strand | P0A988 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 365 | 21% helix, 45% strand | P0A988 |
Ligands and binding sites
- 0LA · (2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid · ligand · chains A
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.43 | 0.74 | 29 | PGE |
| 2 | 70 | 0.37 | 0.78 | 14 | empty |
| 3 | 79 | 0.33 | 0.75 | 17 | empty |
| 4 | 62 | 0.30 | 0.74 | 16 | empty |
| 5 | 50 | 0.29 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1322 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
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 P0A988
- Elsewhere: RCSB PDB 4MJR · PDBe 4MJR · UniProt P0A988
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