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MolNFT v1 · #56065 · protein

Complex structure of lf-transferase and daf

2Z3M · LEUCYL/PHENYLALANYL-tRNA-protein transferase: “Complex structure of lf-transferase and daf”. X-ray diffraction, 2 ligands (3D1, PHE), 3 pockets (best druggability 0.79). MolNFT v1 #56065 on GenesisL1: 3D structure, binding sites and…

PDB
2Z3M
Type
protein
Length
462 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
LEUCYL/PHENYLALANYL-tRNA-protein transferase
EC
2.3.2.6
UniProt
P0A8P1
Ligands
3D1, PHE
Pockets
3 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BLEUCYL/PHENYLALANYL-tRNA-protein transferase (EC 2.3.2.6)protein23133% helix, 26% strandP0A8P1

Ligands and binding sites

  • 3D1 · (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · ligand · 2 copies · chains A, B
  • PHE · Phenylalanine · ligand · 2 copies · chains A, B
  • TAR · D(-)-tartaric acid · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15530.790.8554empty
23450.670.81413D1, PHE
32890.670.82343D1, PHE

Interfaces

1 interface between chains.

  • A–B · 917 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

  • 2Z3M · complex structure of LF-transferase and dAF · the same entry in another collection · chain A against A, TM-score 1.00
  • P0A8P1 · AlphaFold monomer V2.0 prediction for LEUCYL/PHENYLALANYL-tRNA-- protein transferase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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