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MolNFT v1 · #170213 · protein

Crystal structure of ATG16L in complex with GTP-bound RAB33B (Q92L)

6Y09: “Crystal structure of ATG16L in complex with GTP-bound RAB33B (Q92L)”. X-ray diffraction, 3 ligands (GTP, MG, PO4). MolNFT v1 #170213 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6Y09
Type
protein
Length
523 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt
Q9H082, Q8C0J2
Ligands
GTP, MG, PO4

Structure

x-ray diffraction · 3 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A—protein176—Q9H082
C, D—protein86—Q8C0J2
B—protein175—Q9H082

Ligands and binding sites

  • GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
  • MG · Magnesium ion · metal · 2 copies · chains A, B
  • PO4 · Phosphate ion · ion · 4 copies · chains A, C, D, B
  • PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B
  • EDO · 1,2-ethanediol · additive · 2 copies · chains B

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

Compared structures

  • 6Y09 · Crystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L) · the same entry in another collection · chain D against D, TM-score 1.00
  • Q9H082 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-33B (Q9H082) · a predicted model of the same protein · chain B against A, TM-score 0.95
  • Q8C0J2 · AlphaFold monomer V2.0 prediction for autophagy-related protein 16-1 (Q8C0J2) · a predicted model of the same protein · chain C against A, TM-score 0.86

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