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MolNFT v2 · #177504 · protein

YDX in complex with tubulin

7CNM: “YDX in complex with tubulin”. X-ray diffraction at 2.44, 5 ligands (GTP, GDP, ACP). MolNFT v2 #177504 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7CNM
Type
protein
Length
2,190 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
UniProt
Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands
GTP, GDP, ACP, MG, CA

Structure

x-ray diffraction · resolution 2.44 · 6 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein437—Q2XVP4
B—protein429—A0A287AGU7
C—protein440—Q2XVP4
D—protein425—A0A287AGU7
E—protein121—P63042
F—protein338—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
  • ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
  • MG · Magnesium ion · metal · 3 copies · chains B, C
  • 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.

Compared structures

  • 7CNM · Ydx in complex with tubulin · the same entry in another collection · chain C against C, TM-score 1.00
  • 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

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