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Crystal structure of ksp in complex with inhibitor 1

Analyse Crystal structure of ksp in complex with inhibitor 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YRS
Type: protein
Length: 660 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIF11
UniProt: P52732
Ligands: ADP, L47, MG
Pockets: 9 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Kinesin-like protein KIF11	protein	330	34% helix, 27% strand	P52732

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
L47 · 3-[(5S)-1-acetyl-3-(2-chlorophenyl)-4,5-dihydro-1H-pyrazol-5-yl]phenol · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.67	0.75	62	empty
2	354	0.63	0.79	33	empty
3	321	0.61	0.78	34	empty
4	205	0.60	0.81	32	MG, L47
5	144	0.56	0.82	22	L47

Interfaces

1 interface between chains.

A–B · 304 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1YRS · Crystal structure of KSP in complex with inhibitor 1 · the same entry in another collection · chain A against A, TM-score 1.00
P52732 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF11 (P52732) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P52732
Elsewhere: RCSB PDB 1YRS · PDBe 1YRS · UniProt P52732

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