MolNFT v1 · #177584 · protein

Crystal structure of tubulin in complex with tubulysin analogue tgl

7EN3 · Tubulin alpha-1B chain: “Crystal structure of tubulin in complex with tubulysin analogue tgl”. X-ray diffraction, 6 ligands (GTP, GDP, J6R), 20 pockets (best druggability 0.82). MolNFT v1 #177584 on GenesisL1: 3D structure, binding…

PDB: 7EN3
Type: protein
Length: 2,188 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: Q2XVP4, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, J6R, ACP, MG, CA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	46% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	428	48% helix, 19% strand	Q6B856
C	Tubulin alpha-1B chain	protein	440	46% helix, 17% strand	Q2XVP4
D	Tubulin beta-2B chain	protein	424	48% helix, 19% strand	Q6B856
E	Stathmin-4	protein	121	76% helix, 13% strand	P63043
F	Tubulin tyrosine ligase	protein	338	32% helix, 21% 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
J6R · (2S,4R)-5-(4-fluorophenyl)-2-methyl-4-[[2-[(1R,3R)-4-methyl-3-[5-methylhexyl-[(2S,3S)-3-methyl-2-[[(2R)-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-1-oxidanyl-pentyl]-1,3-thiazol-4-yl]carbonylamino]pentanoic acid · ligand · 2 copies · chains B, C, D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, 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	1123	0.82	0.83	104	GDP, MG, J6R
2	1035	0.81	0.82	108	GTP, MG
3	184	0.81	0.96	43	empty
4	1157	0.80	0.82	120	GTP, MG
5	74	0.73	0.97	21	empty

Interfaces

9 interfaces between chains.

A–E · 1677 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1417 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1403 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 907 Å² buried · 17 hydrogen bonds · protein-protein
C–E · 842 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7EN3 · Crystal structure of tubulin in complex with Tubulysin analogue TGL · the same entry in another collection · chain F against F, TM-score 1.00
Q6B856 · AlphaFold monomer V2.0 prediction for tubulin beta-2B chain (Q6B856) · a predicted model of the same protein · chain D against A, TM-score 0.99
Q2XVP4 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (Q2XVP4) · a predicted model of the same protein · chain C against A, TM-score 0.96
P63043 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63043) · a predicted model of the same protein · chain E against A, TM-score 0.78

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 Q6B856
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7EN3 · PDBe 7EN3 · UniProt Q2XVP4 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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