Structure of PDB 5ibq Chain A Binding Site BS01

Receptor Information

>5ibq Chain A (length=287) Species: 347834 (Rhizobium etli CFN 42)

MADLIAIITPAHDNPFFKAEAVGAEAKAKELGYETLVMTHDDDANKQSEM
IDTAIGRGAKAIILDNAGADASVAAVKKAKDAGIPSFLIDREINATGVAV
AQIVSNNYQGAQLGAQEFVKLMGEKGNYVELVGKESDTNAGIRSQGYHDV
IDDYPEMKSVAKQSANWSQTEAYSKMETILQANPDIKGVISGNDTMAMGA
IAALQAAGRKDVIVVGFDGSNDVRDSIKSGGIKATVLQPAYAQAQLAVEQ
ADAYIKNKTTPKEEKQLMDCVLINADNAGKLETFALT

Ligand information

• Ligand ID: XXM
• InChI: InChI=1S/C5H10O5/c6-1-5(9)2-10-4(8)3(5)7/h3-4,6-9H,1-2H2/t3-,4-,5+/m0/s1
• InChIKey: ASNHGEVAWNWCRQ-VAYJURFESA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: C1[C@@]([C@H]([C@H](O1)O)O)(CO)O
  ACDLabs 12.01: OCC1(C(C(OC1)O)O)O
  CACTVS 3.385: OC[C]1(O)CO[CH](O)[CH]1O
  CACTVS 3.385: OC[C@@]1(O)CO[C@H](O)[C@@H]1O
  OpenEye OEToolkits 2.0.4: C1C(C(C(O1)O)O)(CO)O
• Formula: C5 H10 O5
• Name: 3-C-(hydroxylmethyl)-alpha-D-erythrofuranose;
  alpha-D-apiose;
  3-C-(hydroxylmethyl)-alpha-D-erythrose;
  3-C-(hydroxylmethyl)-D-erythrose;
  3-C-(hydroxylmethyl)-erythrose;
  (2S,3R,4R)-4-(hydroxymethyl)oxolane-2,3,4-triol
• ZINC: ZINC000014854290
• PDB chain: 5ibq Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ibq Crystal structure of an ABC solute binding protein from Rhizobium etli CFN 42 (RHE_PF00037,TARGET EFI-511357) in complex with alpha-D-apiose
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): N39 F41 D115 R116 D162 N164 R168 W192 N218 D243
• Binding residue (residue number reindexed from 1): N14 F16 D90 R91 D137 N139 R143 W167 N193 D218
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:5ibq, PDBe:5ibq, PDBj:5ibq
• PDBsum: 5ibq
• UniProt: Q2JZQ5|APIBP_RHIEC D-apiose import binding protein (Gene Name=RHE_PF00037)