MolNFT v1 · #126111 · protein

Nucleotide-free kinesin-1 motor domain, P1 crystal form

5LT2 · Kinesin-like protein: “Nucleotide-free kinesin-1 motor domain, P1 crystal form”. X-ray diffraction, 1 ligand (SO4), 19 pockets (best druggability 0.73). MolNFT v1 #126111 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LT2
Type: protein
Length: 1,856 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein
UniProt: Q6P164
Ligands: SO4
Pockets: 19 · best druggability 0.73

Structure

x-ray diffraction · 6 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-like protein	protein	314	32% helix, 28% strand	Q6P164
B	Kinesin-like protein	protein	307	33% helix, 28% strand	Q6P164
C	Kinesin-like protein	protein	308	30% helix, 29% strand	Q6P164
D	Kinesin-like protein	protein	313	32% helix, 30% strand	Q6P164
E	Kinesin-like protein	protein	307	30% helix, 31% strand	Q6P164
K	Kinesin-like protein	protein	307	32% helix, 30% strand	Q6P164

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, E, K

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

Pockets

19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	820	0.73	0.78	105	SO4
2	579	0.64	0.76	52	empty
3	467	0.63	0.76	56	SO4
4	469	0.62	0.76	44	empty
5	251	0.62	0.81	38	empty

Interfaces

9 interfaces between chains.

C–E · 672 Å² buried · 20 hydrogen bonds · protein-protein
A–K · 624 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 524 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 439 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 438 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5LT2 · nucleotide-free kinesin-1 motor domain, P1 crystal form · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6P164
Elsewhere: RCSB PDB 5LT2 · PDBe 5LT2 · UniProt Q6P164

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