Research workbench
DNA polymerase sliding clamp from escherichia COLI with peptide 20 bound
Analyse DNA polymerase sliding clamp from escherichia COLI with peptide 20 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AZD
- Type
- protein
- Length
- 1,479 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; Peptide 20
- UniProt
- A0A073FMV0
- Ligands
- SGZ, GLN
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 367 | 21% helix, 46% strand | A0A073FMV0 |
| B | Beta sliding clamp | protein | 365 | 21% helix, 45% strand | A0A073FMV0 |
| C | Beta sliding clamp | protein | 368 | 21% helix, 45% strand | A0A073FMV0 |
| D | Beta sliding clamp | protein | 363 | 21% helix, 46% strand | A0A073FMV0 |
| H, I, J, K | Peptide 20 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- SGZ · 2-naphthalen-1-ylethanal · ligand · 4 copies · chains A, C, H, J, B, D, I, K
- GLN · Glutamine · ligand · 4 copies · chains A, H, B, D, I, C, J, K
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.71 | 0.75 | 93 | PEG, SGZ, GLN |
| 2 | 1138 | 0.71 | 0.75 | 111 | 1PE, SGZ, GLN |
| 3 | 593 | 0.63 | 0.74 | 49 | SGZ, GLN |
| 4 | 581 | 0.62 | 0.74 | 65 | empty |
| 5 | 361 | 0.55 | 0.74 | 53 | PEG |
Interfaces
12 interfaces between chains.
- A–D · 1335 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1298 Ų buried · 36 hydrogen bonds · protein-protein
- C–J · 468 Ų buried · 6 hydrogen bonds · protein-protein
- D–K · 449 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 446 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 7AZD · DNA polymerase sliding clamp from Escherichia coli with peptide 20 bound · 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 A0A073FMV0
- Elsewhere: RCSB PDB 7AZD · PDBe 7AZD · UniProt A0A073FMV0
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