MolNFT v1 · #126112 · protein

Nucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form

5LT3 · Kinesin-1 heavy chain: “Nucleotide-free kinesin-1 motor domain T87A mutant, P1 crystal form”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.70). MolNFT v1 #126112 on GenesisL1: 3D structure, binding sites and…

PDB: 5LT3
Type: protein
Length: 1,843 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 0.70

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kinesin-1 heavy chain	protein	307	32% helix, 29% strand	P33176
B	Kinesin-1 heavy chain	protein	305	32% helix, 30% strand	P33176
C	Kinesin-1 heavy chain	protein	300	31% helix, 29% strand	P33176
D	Kinesin-1 heavy chain	protein	311	32% helix, 29% strand	P33176
E	Kinesin-1 heavy chain	protein	308	31% helix, 30% strand	P33176
K	Kinesin-1 heavy chain	protein	312	32% helix, 28% strand	P33176

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	435	0.70	0.81	71	SO4
2	637	0.66	0.75	62	empty
3	345	0.64	0.79	52	SO4
4	440	0.61	0.76	46	empty
5	250	0.59	0.79	44	SO4

Interfaces

8 interfaces between chains.

C–E · 666 Å² buried · 22 hydrogen bonds · protein-protein
A–K · 620 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 522 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 475 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 442 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5LT3 · nucleotide-free kinesin-1 motor domain T87A 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 0.93

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 5LT3 · PDBe 5LT3 · UniProt P33176

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