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Crystal structure of the KIF5C motor domain with ADP

Analyse Crystal structure of the KIF5C motor domain with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X2T
Type: protein
Length: 637 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin heavy chain isoform 5C
UniProt: P28738
Ligands: ADP
Pockets: 7 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin heavy chain isoform 5C	protein	311	28% helix, 28% strand	P28738
B	Kinesin heavy chain isoform 5C	protein	326	32% helix, 29% strand	P28738

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

7 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	551	0.68	0.78	79	empty
2	177	0.61	0.83	37	empty
3	109	0.49	0.81	21	empty
4	126	0.44	0.77	26	ADP
5	59	0.39	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 959 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3X2T · Crystal Structure of the KIF5C Motor Domain With ADP · the same entry in another collection · chain A against A, TM-score 1.00
P28738 · AlphaFold monomer V2.0 prediction for kinesin heavy chain isoform 5C (P28738) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P28738
Elsewhere: RCSB PDB 3X2T · PDBe 3X2T · UniProt P28738

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