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MolNFT v1 · #176063 · protein

Epd in complex with tubulin

7DAD: “Epd in complex with tubulin”. X-ray diffraction, 7 ligands (GTP, GDP, EPD). MolNFT v1 #176063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7DAD
Type
protein
Length
2,209 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands
GTP, GDP, EPD, ACP, MG, CA, CL

Structure

x-ray diffraction · 6 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein438—Q2XVP4
B—protein428—A0A287AGU7
C—protein440—Q2XVP4
D—protein431—A0A287AGU7
E—protein121—P63042
F—protein351—E1BQ43

Ligands and binding sites

  • GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
  • GDP · Guanosine-5'-diphosphate · ligand · chains B
  • EPD · Epothilone D · ligand · chains D
  • ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
  • MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
  • CA · Calcium ion · metal · 4 copies · chains A, B, C
  • CL · Chloride ion · ion · chains A
  • 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

  • 7DAD · EPD 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 0.75

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