Research workbench
E. COLI sliding clamp in complex with (R)-6-bromo-9-(2- (carboxymethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2- carboxylic acid
Analyse E. COLI sliding clamp in complex with (R)-6-bromo-9-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OVH
- Type
- protein
- Length
- 728 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
- U6NCW5
- Ligands
- 2VE, CA, CL
- Pockets
- 4 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 362 | 23% helix, 45% strand | U6NCW5 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 366 | 22% helix, 46% strand | U6NCW5 |
Ligands and binding sites
- 2VE · (2R)-6-bromo-9-{2-[(carboxymethyl)amino]-2-oxoethyl}-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.30 | 0.76 | 15 | empty |
| 2 | 53 | 0.28 | 0.74 | 14 | empty |
| 3 | 54 | 0.27 | 0.74 | 16 | empty |
| 4 | 58 | 0.27 | 0.73 | 18 | PG4 |
Interfaces
1 interface between chains.
- A–B · 1333 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4OVH · E. coli sliding clamp in complex with (R)-6-bromo-9-(2-(carboxymethylamino)-2-oxoethyl)-2… · the same entry in another collection · chain A against A, TM-score 1.00
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 U6NCW5
- Elsewhere: RCSB PDB 4OVH · PDBe 4OVH · UniProt U6NCW5
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