Structure of PDB 5dkv Chain D Binding Site BS01

Receptor Information

>5dkv Chain D (length=298) Species: 311402 (Allorhizobium ampelinum S4)

KFRIALIPGLTTDAFYITMHKGAEAAAAAIGAQIIFQGAPDFNPVTQVPV
LDAVIAKKPDAILIAPTDTTQLVQPLKKAADAGIPMITVDTFIGTGDYQT
GAGDGDFPLSYIASDNVLGGEIAARSLALAIGDKGKVYVSNVKPGVSTTD
QREQGFKSEMAKHPGITVLETQFNDNDANKAASQLQAVYARNPDLAGVFG
ANLFSGLGSANGVQQAGQSGTIKVVAFDAPGSVVDNLKSGLIDFAIAQHP
AEIGYYGVISAYAHLTGQSIPTKIGTGFTVINKSNVTDPAVARFIYAE

Ligand information

• Ligand ID: T6T
• InChI: InChI=1S/C6H12O6/c7-2-6(11)5(10)4(9)3(8)1-12-6/h3-5,7-11H,1-2H2/t3-,4+,5+,6+/m1/s1
• InChIKey: LKDRXBCSQODPBY-VANKVMQKSA-N
• SMILES:
  CACTVS 3.385: OC[C]1(O)OC[CH](O)[CH](O)[CH]1O
  ACDLabs 12.01: OC1C(OCC(C1O)O)(CO)O
  CACTVS 3.385: OC[C@]1(O)OC[C@@H](O)[C@H](O)[C@@H]1O
  OpenEye OEToolkits 2.0.6: C1[C@H]([C@@H]([C@@H]([C@@](O1)(CO)O)O)O)O
  OpenEye OEToolkits 2.0.6: C1C(C(C(C(O1)(CO)O)O)O)O
• Formula: C6 H12 O6
• Name: alpha-D-tagatopyranose;
  alpha-D-tagatose;
  D-tagatose;
  tagatose
• ChEMBL: CHEMBL3183898
• ZINC: ZINC000003830878
• PDB chain: 5dkv Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dkv Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET EFI-511225) bound with alpha-D-Tagatopyranose
• Resolution: 1.68 Å
• Binding residue (original residue number in PDB): D44 F46 D121 T179 R183 N233 L234 D259 Q279
• Binding residue (residue number reindexed from 1): D13 F15 D90 T148 R152 N202 L203 D228 Q248
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0004712 protein serine/threonine/tyrosine kinase activity
• GO:0030246 carbohydrate binding

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:5dkv, PDBe:5dkv, PDBj:5dkv
• PDBsum: 5dkv
• UniProt: B9K0T2