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MolNFT v1 · #176092 · protein

IC1 in complex with tubulin

7DB9: “IC1 in complex with tubulin”. X-ray diffraction, 6 ligands (GTP, GDP, IC1). MolNFT v1 #176092 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7DB9
Type
protein
Length
2,207 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands
GTP, GDP, IC1, ACP, MG, CA

Structure

x-ray diffraction · 6 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein439—Q2XVP4
B—protein430—A0A287AGU7
C—protein440—Q2XVP4
D—protein422—A0A287AGU7
E—protein124—P63042
F—protein352—E1BQ43

Ligands and binding sites

  • GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, D
  • GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
  • IC1 · 3-[(2,4,6-trimethoxy-phenyl)-methylene]-indolin-2-one · ligand · 2 copies · chains A, B, C, D
  • ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
  • MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
  • CA · Calcium ion · metal · 4 copies · chains A, E, B, C
  • MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Compared structures

  • 7DB9 · IC1 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 0.76

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