Research workbench
E. COLI sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H- carbazole-7-carboxylic acid
Analyse E. COLI sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N99
- Type
- protein
- Length
- 721 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
- 2J1, CA
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 356 | 22% helix, 45% strand | P0A988 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 365 | 22% helix, 45% strand | P0A988 |
Ligands and binding sites
- 2J1 · 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid · ligand · chains A
- CA · Calcium ion · metal · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 19 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.43 | 0.74 | 34 | PG4, PEG |
| 2 | 71 | 0.32 | 0.75 | 18 | PEG |
Interfaces
1 interface between chains.
- A–B · 1303 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4N99 · E. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxyli… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A988 · AlphaFold monomer V2.0 prediction for beta sliding clamp (P0A988) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 4N99 · PDBe 4N99 · UniProt P0A988
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