MolNFT v1 · #84280 · protein

Crystal structure of the tpr domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide

3ZFW: “Crystal structure of the tpr domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide”. X-ray diffraction, 5 pockets (best druggability 0.48). MolNFT v1 #84280 on GenesisL1: 3D structure, binding sites and…

PDB: 3ZFW
Type: protein
Length: 472 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin light chain 2; Pleckstrin homology domain-containing family M member 2
UniProt: Q91YS4, Q8IWE5
Pockets: 5 · best druggability 0.48

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin light chain 2	protein	226	78% helix, 0% strand	Q91YS4
B	Kinesin light chain 2	protein	225	77% helix, 0% strand	Q91YS4
X	Pleckstrin homology domain-containing family M member 2	protein	11	0% helix, 0% strand	Q8IWE5
Y	Pleckstrin homology domain-containing family M member 2	protein	10	0% helix, 0% strand	Q8IWE5

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.48	0.80	17	empty
2	76	0.48	0.82	18	empty
3	103	0.45	0.79	17	empty
4	86	0.34	0.75	18	empty
5	66	0.30	0.74	17	empty

Interfaces

3 interfaces between chains.

A–X · 808 Å² buried · 12 hydrogen bonds · protein-protein
B–Y · 797 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 483 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3ZFW · Crystal structure of the TPR domain of kinesin light chain 2 in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
Q8IWE5 · AlphaFold monomer V2.0 prediction for pleckstrin homology domain- containing family M… · a predicted model of the same protein · chain Y against A, TM-score 0.35

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 Q91YS4
Every structure of UniProt Q8IWE5
Elsewhere: RCSB PDB 3ZFW · PDBe 3ZFW · UniProt Q91YS4 · UniProt Q8IWE5

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