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Crystal structure of the KIFC3 motor domain in complex with ADP

Analyse Crystal structure of the KIFC3 motor domain in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WDE
Type: protein
Length: 320 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIFC3
UniProt: Q9BVG8
Ligands: ADP, MG, UNX
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-like protein KIFC3	protein	320	33% helix, 28% strand	Q9BVG8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
UNX · Unknown atom or ion · ion · 46 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.68	0.83	42	MG, UNX
2	163	0.53	0.80	22	UNX
3	80	0.37	0.77	18	UNX

Compared structures

5WDE · Crystal structure of the KIFC3 motor domain in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
Q9BVG8 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIFC3 (Q9BVG8) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9BVG8
Elsewhere: RCSB PDB 5WDE · PDBe 5WDE · UniProt Q9BVG8

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