MolNFT v1 · #111178 · protein

Crystal structure of tubulin bound to compound 2

4YJ3 · Tubulin alpha-1B chain: “Crystal structure of tubulin bound to compound 2”. X-ray diffraction, 5 ligands (GTP, GDP, 4EE), 20 pockets (best druggability 0.85). MolNFT v1 #111178 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4YJ3
Type: protein
Length: 2,124 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin-tyrosine ligase
UniProt: P81947, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, 4EE, MG, CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	438	42% helix, 16% strand	P81947
B	Tubulin beta-2B chain	protein	422	47% helix, 19% strand	Q6B856
C	Tubulin alpha-1B chain	protein	440	43% helix, 17% strand	P81947
D	Tubulin beta-2B chain	protein	421	46% helix, 19% strand	Q6B856
E	Stathmin-4	protein	121	76% helix, 14% strand	P63043
F	Tubulin-tyrosine ligase	protein	282	31% helix, 22% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
4EE · 6-(4-ethoxyphenyl)-3-(2-methoxyphenyl)-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazine · ligand · 2 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 3 copies · chains A, B, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
IMD · Imidazole · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	979	0.85	0.86	93	MG, GTP, 4EE
2	564	0.83	0.88	63	4EE
3	653	0.82	0.87	89	GDP, MG
4	174	0.80	0.95	36	empty
5	441	0.77	0.86	57	MG, GTP

Interfaces

9 interfaces between chains.

A–E · 1551 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1519 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1334 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 941 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 833 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4YJ3 · Crystal structure of tubulin bound to compound 2 · 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 P81947
Every structure of UniProt Q6B856
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 4YJ3 · PDBe 4YJ3 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.