MolNFT v1 · #10410 · protein

Crystal structure of the clamp loader small subunit from pyrococcus furiosus

1IQP · Rfcs: “Crystal structure of the clamp loader small subunit from pyrococcus furiosus”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.75). MolNFT v1 #10410 on GenesisL1: 3D structure, binding sites and pockets in…

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.

Pocket	Volume (Å³)	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 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1936 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 1912 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1711 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1693 Å² 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

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