Research workbench
E. COLI sliding clamp in complex with acqlalf
Analyse E. COLI sliding clamp in complex with acqlalf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3P
- Type
- protein
- Length
- 718 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit beta; (ACE)QLALF
- EC
- 2.7.7.7
- UniProt
- P0A988
- Ligands
- ACE, CA, CL
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 357 | 22% helix, 45% strand | P0A988 |
| B | DNA polymerase III subunit beta (EC 2.7.7.7) | protein | 356 | 21% helix, 47% strand | P0A988 |
| E | (ACE)QLALF | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, E
- CA · Calcium ion · metal · 5 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · chains A
- PG4 · Tetraethylene glycol · 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
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 | 50 | 0.40 | 0.83 | 18 | empty |
| 2 | 63 | 0.30 | 0.74 | 19 | PG4 |
| 3 | 59 | 0.29 | 0.75 | 15 | empty |
| 4 | 58 | 0.28 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1343 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 472 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 4K3P · PDBe 4K3P · UniProt P0A988
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