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KIF14[391-772] dimer two-heads-bound state - ADP-alfx in complex with a microtubule

Analyse KIF14[391-772] dimer two-heads-bound state - ADP-alfx in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WWG
Type: protein
Length: 2,479 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kinesin-like protein KIF14; Tubulin alpha-1B chain; Tubulin beta-2B chain
UniProt: L0N7N1, Q2XVP4, A0A287AGU7
Ligands: ADP, GTP, GDP, TA1, AF3, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Kinesin-like protein KIF14	protein	367	29% helix, 29% strand	L0N7N1
A, E	Tubulin alpha-1B chain	protein	441	42% helix, 16% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	434	46% helix, 19% strand	A0A287AGU7
N	Kinesin-like protein KIF14	protein	365	29% helix, 27% strand	L0N7N1
I	Tubulin beta-2B chain	protein	431	47% helix, 18% strand	A0A287AGU7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains K, N
GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, E, I
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, E, I
TA1 · Taxol · ligand · 2 copies · chains B, I
AF3 · Aluminum fluoride · ligand · chains K
MG · Magnesium ion · metal · 3 copies · chains K, A, B, E, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.84	0.95	48	GDP
2	264	0.84	0.95	43	GTP, MG
3	264	0.83	0.95	42	GTP, MG
4	1033	0.79	0.81	74	empty
5	1026	0.78	0.80	69	empty

Interfaces

8 interfaces between chains.

E–I · 2045 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2022 Å² buried · 24 hydrogen bonds · protein-protein
B–E · 1943 Å² buried · 24 hydrogen bonds · protein-protein
N–E · 813 Å² buried · 4 hydrogen bonds · protein-protein
K–A · 780 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6WWG · KIF14[391-772] dimer two-heads-bound state - ADP-AlFx in complex with a microtubule · the same entry in another collection · chain I against I, TM-score 1.00
L0N7N1 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF14 (L0N7N1) · a predicted model of the same protein · chain K against A, TM-score 0.94

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 L0N7N1
Every structure of UniProt Q2XVP4
Every structure of UniProt A0A287AGU7
Elsewhere: RCSB PDB 6WWG · PDBe 6WWG · UniProt L0N7N1 · UniProt Q2XVP4 · UniProt A0A287AGU7

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