MolNFT v1 · #126113 · protein

Nucleotide-free kinesin-1 motor domain T92V mutant, P1 crystal form

5LT4 · Kinesin-1 heavy chain: “Nucleotide-free kinesin-1 motor domain T92V mutant, P1 crystal form”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.68). MolNFT v1 #126113 on GenesisL1: 3D structure, binding sites and…

PDB: 5LT4
Type: protein
Length: 1,852 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-1 heavy chain
UniProt: P33176
Ligands: SO4
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-1 heavy chain	protein	313	31% helix, 30% strand	P33176
B	Kinesin-1 heavy chain	protein	308	33% helix, 30% strand	P33176
C	Kinesin-1 heavy chain	protein	308	31% helix, 30% strand	P33176
D	Kinesin-1 heavy chain	protein	311	32% helix, 31% strand	P33176
E	Kinesin-1 heavy chain	protein	305	31% helix, 31% strand	P33176
K	Kinesin-1 heavy chain	protein	307	32% helix, 30% strand	P33176

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, K

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	430	0.68	0.80	60	SO4
2	218	0.64	0.83	39	SO4
3	178	0.61	0.82	28	SO4
4	382	0.60	0.77	40	empty
5	199	0.60	0.82	32	SO4

Interfaces

9 interfaces between chains.

C–E · 696 Å² buried · 21 hydrogen bonds · protein-protein
A–K · 589 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 509 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 444 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 443 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5LT4 · nucleotide-free kinesin-1 motor domain T92V mutant, P1 crystal form · the same entry in another collection · chain K against K, TM-score 1.00
P33176 · AlphaFold monomer V2.0 prediction for kinesin-1 heavy chain (P33176) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 P33176
Elsewhere: RCSB PDB 5LT4 · PDBe 5LT4 · UniProt P33176

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