Research workbench
Crystal structure of a dnan sliding clamp (DNA polymerase III subunit beta) from bartonella birtlesii bound to griselimycin
Analyse Crystal structure of a dnan sliding clamp (DNA polymerase III subunit beta)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PTR
- Type
- protein
- Length
- 762 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta sliding clamp; ACE-mva-MP8-nzc-leu-MP8-leu-mva-pro-mlu-gly
- UniProt
- J1IY24
- Ligands
- ACE, IOD
- Pockets
- 7 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta sliding clamp | protein | 370 | 24% helix, 44% strand | J1IY24 |
| X, Y | ACE-mva-MP8-nzc-leu-MP8-leu-mva-pro-mlu-gly | protein | 10 | 0% helix, 0% strand | — |
| B | Beta sliding clamp | protein | 372 | 23% helix, 43% strand | J1IY24 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, X, B, Y
- IOD · Iodide ion · ion · 11 copies · chains A, X, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.39 | 0.78 | 20 | EDO |
| 2 | 72 | 0.37 | 0.78 | 21 | EDO |
| 3 | 100 | 0.33 | 0.72 | 21 | empty |
| 4 | 50 | 0.32 | 0.77 | 17 | IOD |
| 5 | 69 | 0.31 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1168 Ų buried · 31 hydrogen bonds · protein-protein
- B–Y · 662 Ų buried · 2 hydrogen bonds · protein-protein
- A–X · 609 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 2 covalent (nonstandard, methylation, covalent ligand).
Compared structures
- 6PTR · Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from… · 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 J1IY24
- Elsewhere: RCSB PDB 6PTR · PDBe 6PTR · UniProt J1IY24
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