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Ligand · RIB

RIB · alpha-D-ribofuranose

RIB, alpha-D-ribofuranose (C5 H10 O5, 150.1 g/mol), in the MolNFT structures on GenesisL1: bound in 13 records (11 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found with it.

Component
RIB
Formula
C5 H10 O5
Class
ligand
Structures
13
PDB entries
11

Binding sites

RIB in 13 structures; the first of them:

  • 4XDA · Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium ion. · RIB A401 · binds ASN11, ASP13, GLY38, GLY39, LYS40, ASN43, ALA95, ILE97 and 8 more
  • 5WV1 · Crystal structure of the complex of Ribosome inactivating protein from Momordica… · RIB A303 · binds TYR70, ILE71, GLY109, ASN110, TYR111, ILE155, GLU160, ARG163
  • 6WK0 · Crystal structure of human ribokinase in complex with AMPPCP and ribose · RIB B401 · binds MET25, ASP27, GLY52, GLY53, LYS54, ASN57, ALA109, ILE111 and 6 more
  • 8B9Y · Cysteine Synthase from Trypanosoma cruzi with PLP and OAS · RIB A702 · binds CYS56, GLU57, ASN58, PRO59, ALA61, TYR316, CYS56, GLU57 and 4 more
  • 8VAU · Nicotinamide Riboside and CD38: Covalent Inhibition and Live-Cell Labeling · RIB A402 · binds LEU123, LEU124, TRP125, THR144, LEU145, GLU146, SER193, PHE196 and 2 more
  • 9GN2 · Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with ribose… · RIB A202 · binds TYR7, PHE8, GLY9, ALA10, GLY11, TRP12, PHE13, PRO42 and 7 more
  • 5M93 · Crystal structure of sdea-modified ubiquitin. · RIB B101 · binds ASP39, ARG42, ARG72
  • 5WV1 · Crystal structure of the complex of ribosome inactivating protein from momordica… · RIB A303 · binds TYR70, GLY109, ASN110, TYR111, ILE155, GLU160, ARG163
  • 6A89 · Crystal structure of the ternary complex of peptidoglycan recognition protein (pgrp-S)… · RIB D203 · binds SER139, ASN140, HIS168, TYR32, THR97, TRP98, ILE101
  • 6EGW · Crystal structure of the protein-kinase a catalytic subunit from criteculus griseus in… · RIB B101 · binds ASP12, SER16
  • 6ILS · Structure of arabidopsis thaliana ribokinase complexed with ribose and ATP · RIB B402 · binds ASN78, ASP80, GLY105, GLY106, LYS107, ASN110, GLU210, ASP325
  • 6WK0 · Crystal structure of human ribokinase in complex with amppcp and ribose · RIB B401 · binds MET25, ASP27, GLY52, GLY53, LYS54, ASN57, ALA109, GLU154 and 3 more
  • 6ZK3 · Plant nucleoside hydrolase - ZMNRH2B in complex with ribose · RIB A402 · binds ASP18, ASP22, ASP23, ASN47, LEU133, LEU159, ASN168, GLU174 and 4 more

Residues it binds most

ASP 18, ASN 19, GLY 11, GLU 20, ALA 15, LEU 9, THR 10, ILE 8, LYS 8, TYR 5 (residue and the binding sites it lines).

Found with

  • NA · Sodium ion
  • GOL · Glycerol
  • ACP · Phosphomethylphosphonic acid adenylate ester
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose
  • EDO · 1,2-ethanediol
  • 9LQ · [2-[(4-isoquinolin-5-ylsulfonyl-1,4-diazepan-1-yl) methyl]phenyl]boronic acid
  • ADP · Adenosine-5'-diphosphate
  • API · 2,6-diaminopimelic acid
  • ATP · Adenosine-5'-triphosphate
  • CYT · 6-aminopyrimidin-2(1H)-one
  • NNR · Nicotinamide riboside
  • OAS · O-acetylserine

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