Research workbench

YDX in complex with tubulin

Analyse YDX in complex with tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CNM
Type: protein
Length: 2,188 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.44
Source: Gallus gallus; Mus musculus; Sus scrofa
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands: GTP, GDP, G70, ACP, MG, CA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.44 · 6 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	45% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	428	48% helix, 18% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	47% helix, 17% strand	Q2XVP4
D	Tubulin beta chain	protein	424	49% helix, 20% strand	A0A287AGU7
E	Stathmin-4	protein	121	77% helix, 12% strand	P63042
F	Tubulin tyrosine ligase	protein	338	31% 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
G70 · (2~{S},4~{S})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-4-methyl-3-[[(2~{S},3~{S})-3-methyl-2-[[(2~{R})-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-cyclohexyl-2-methyl-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 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.81	0.96	42	empty
2	1015	0.81	0.82	99	GDP, MG, G70
3	1069	0.81	0.82	109	GTP, MG
4	911	0.80	0.82	91	GTP, MG
5	815	0.72	0.78	59	empty

Interfaces

9 interfaces between chains.

A–E · 1675 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1424 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1402 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 888 Å² buried · 18 hydrogen bonds · protein-protein
C–E · 815 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7CNM · Ydx in complex with tubulin · the same entry in another collection · chain F against F, TM-score 1.00
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
P63042 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63042) · a predicted model of the same protein · chain E against A, TM-score 0.77

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 A0A287AGU7
Every structure of UniProt P63042
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7CNM · PDBe 7CNM · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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