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Ligand · U

U · Uridine-5'-monophosphate

U, Uridine-5'-monophosphate (C9 H13 N2 O9 P, 324.2 g/mol), in the MolNFT structures on GenesisL1: bound in 38 records (23 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found…

Component
U
Formula
C9 H13 N2 O9 P
Class
ligand
Structures
38
PDB entries
23

Binding sites

U in 38 structures; the first of them:

  • 5L8Q · Structure of deformed wing virus, a honeybee pathogen · U C501 · binds VAL27, PRO29
  • 5LMO · Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1B) · U W102 · binds G1710, ARG46, ARG125
  • 5MV5 · Structure of deformed wing virus, a honeybee pathogen · U C501 · binds VAL27, PRO29
  • 5MV6 · Structure of deformed wing virus, a honeybee pathogen · U C501 · binds VAL27, PRO29
  • 6G63 · RNase E in complex with sRNA RrpA · U N601 · binds VAL128, MET130, SER140, ARG142, ILE167, ARG169, THR170, ARG223 and 1 more
  • 6TRQ · S.c. Scavenger Decapping Enzyme DcpS in complex with the capped RNA dinucleotide m7G-GU · U A402 · binds ASP22, ASN24, PHE132, GLY280, ASN281, SER282, ALA314, ARG255 and 3 more
  • 6YVL · Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution… · U A502 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 11 more
  • 6YVM · Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution… · U A502 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 11 more
  • 6YVN · Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution… · U A502 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 11 more
  • 6ZX0 · OMPD-domain of human UMPS in complex with the substrate OMP at 1.25 Angstroms resolution · U A502 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, MET371, SER372 and 7 more
  • 7OQF · Human OMPD-domain of UMPS in complex with OMP at 1.05 Angstrom resolution, 5 minutes… · U A505 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 14 more
  • 7OQI · Human OMPD-domain of UMPS in complex with substrate OMP at 1.15 Angstrom resolution, 10… · U A505 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 14 more
  • 7OQK · Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 Angstroms resolution, 15… · U A505 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 14 more
  • 7OQM · Human OMPD-domain of UMPS in complex with substrate OMP at 1.05 Angstroms resolution, 20… · U A505 · binds SER257, ASP259, LYS281, HIS283, ASP312, ALY314, GLU370, MET371 and 14 more
  • 7PB5 · Crystal structure of CD73 in complex with UMP in the open form · U A606 · binds ARG354, ASN390, GLY392, GLY393, ARG395, PHE417, GLY447, PHE500 and 1 more
  • 7PD3 · Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7… · U 4202 · binds PHE66, ARG85, TYR89, ARG101, U3012, G3013, G3382, A3383 and 1 more

Residues it binds most

ASP 46, ARG 60, ILE 36, SER 35, GLY 41, LYS 45, VAL 40, TYR 49, HIS 45, PRO 36 (residue and the binding sites it lines).

Found with

  • SO4 · Sulfate ion
  • GOL · Glycerol
  • OMP · Orotidine-5'-monophosphate
  • ZN · Zinc ion
  • MG · Magnesium ion
  • A · Adenosine-5'-monophosphate
  • 0G · L-guanosine-5'-monophosphate
  • 2PO · Phosphonate
  • G · Guanosine-5'-monophosphate
  • M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate
  • CA · Calcium ion
  • C · Cytidine-5'-monophosphate

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