MolNFT v1 · #68164 · protein

Cryo-EM structure of dynamic GDP-microtubule (14 protofilaments) decorated with kinesin

3JAS · Tubulin alpha-1B chain: “Cryo-EM structure of dynamic GDP-microtubule (14 protofilaments) decorated with kinesin”. Electron microscopy, 3 ligands (GTP, GDP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #68164 on GenesisL1: 3D…

PDB: 3JAS
Type: protein
Length: 5,124 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain
UniProt: Q2XVP4, P02554
Ligands: GTP, GDP, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 48% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, J, C, L, A, K	Tubulin alpha-1B chain	protein	428	48% helix, 18% strand	Q2XVP4
F, G, D, I, B, H	Tubulin beta chain	protein	426	49% helix, 19% strand	P02554

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains E, G, F, J, C, I, D, L, A, H, B, K
GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains E, F, G, C, D, I, A, B, H
MG · Magnesium ion · metal · 6 copies · chains E, G, F, J, C, I, D, L, A, H, B, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	251	0.84	0.96	47	GTP, MG
2	256	0.83	0.95	47	GTP, MG
3	257	0.83	0.95	47	GTP, MG
4	246	0.83	0.95	46	GTP, MG
5	255	0.83	0.95	46	GTP, MG

Interfaces

17 interfaces between chains.

D–L · 1836 Å² buried · 20 hydrogen bonds · protein-protein
F–J · 1829 Å² buried · 20 hydrogen bonds · protein-protein
B–K · 1826 Å² buried · 21 hydrogen bonds · protein-protein
C–I · 1826 Å² buried · 19 hydrogen bonds · protein-protein
A–H · 1822 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3JAS · Cryo-EM structure of dynamic GDP-microtubule (14 protofilaments) decorated with kinesin · the same entry in another collection · chain E against E, 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 Q2XVP4
Every structure of UniProt P02554
Elsewhere: RCSB PDB 3JAS · PDBe 3JAS · UniProt Q2XVP4 · UniProt P02554

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