Research workbench
Crystal structure of the clamp loader small subunit from pyrococcus furiosus
Analyse Crystal structure of the clamp loader small subunit from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IQP
- Type
- protein
- Length
- 1,949 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rfcs
- UniProt
- Q8U4J3
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Rfcs | protein | 326 | 62% helix, 10% strand | Q8U4J3 |
| C | Rfcs | protein | 319 | 56% helix, 10% strand | Q8U4J3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.75 | 0.79 | 80 | empty |
| 2 | 682 | 0.74 | 0.80 | 71 | empty |
| 3 | 924 | 0.72 | 0.77 | 83 | empty |
| 4 | 512 | 0.72 | 0.81 | 48 | ADP |
| 5 | 531 | 0.71 | 0.80 | 58 | empty |
Interfaces
10 interfaces between chains.
- C–F · 2090 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1936 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1912 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1711 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1693 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1IQP · Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus · the same entry in another collection · chain F against F, TM-score 1.00
- Q8U4J3 · AlphaFold monomer V2.0 prediction for replication factor C small subunit (Q8U4J3) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 Q8U4J3
- Elsewhere: RCSB PDB 1IQP · PDBe 1IQP · UniProt Q8U4J3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.