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MolNFT v1 · #176065 · protein

Ixa in complex with tubulin

7DAF: “Ixa in complex with tubulin”. X-ray diffraction, 7 ligands (GTP, GDP, GZX). MolNFT v1 #176065 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
7DAF
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, GZX, ACP, MG, CA, CL

Structure

x-ray diffraction · 6 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein442—Q2XVP4
B—protein423—A0A287AGU7
C—protein440—Q2XVP4
D—protein430—A0A287AGU7
E—protein123—P63042
F—protein351—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
  • GZX · (1~{S},3~{S},7~{S},10~{R},11~{S},12~{S},16~{R})-8,8,10, 12,16-pentamethyl-3-[(~{E})-1-(2-methyl-1,3-thiazol-4-yl)prop-1-en-2-yl]-7,11-bis(oxidanyl)-17-oxa-4-azabicyclo[14.1.0]heptadecane-5,9-dione · ligand · chains D
  • ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A, F
  • MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, F
  • CA · Calcium ion · metal · 4 copies · chains A, B, C, E
  • 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

  • 7DAF · IXA 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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