Research workbench
Crystal structure of an inactivated ssp siclopps intein with cfahpq extein
Analyse Crystal structure of an inactivated ssp siclopps intein with cfahpq extein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OL5
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit ALPHA,DNA polymerase III subunit alpha
- EC
- 2.7.7.7
- UniProt
- P74750
- Ligands
- CO
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase III subunit ALPHA,DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 140 | 9% helix, 54% strand | P74750 |
| C, D | DNA polymerase III subunit ALPHA,DNA polymerase III subunit alpha (EC 2.7.7.7) | protein | 140 | 11% helix, 50% strand | P74750 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.54 | 0.73 | 49 | empty |
| 2 | 90 | 0.53 | 0.84 | 17 | empty |
| 3 | 302 | 0.51 | 0.73 | 30 | empty |
| 4 | 181 | 0.48 | 0.76 | 29 | empty |
| 5 | 137 | 0.45 | 0.77 | 17 | PG4 |
Interfaces
5 interfaces between chains.
- A–D · 1050 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 366 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 156 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 103 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 100 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5OL5 · Crystal structure of an inactivated Ssp SICLOPPS intein with CFAHPQ extein · the same entry in another collection · chain D against D, TM-score 1.00
- P74750 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit alpha (P74750) · a predicted model of the same protein · chain B against A, TM-score 0.67
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 P74750
- Elsewhere: RCSB PDB 5OL5 · PDBe 5OL5 · UniProt P74750
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