Structure of PDB 2ygm Chain A Binding Site BS03

Receptor Information

>2ygm Chain A (length=351) Species: 406556 (Streptococcus pneumoniae SP3-BS71)

HMASTYLSDMDWSSATHGDIDKTKTVQKDAPFTTGNKGEHTKISLLTSDD
KVKYFDKGIGTVADSPSVISYDISGQGFEKFETYIGIDQSANSSRSDHAV
VDRIEIEIDGKVVYSSSVTNPEGFRYNTQAQFISVTIPQNAKKISLKSFA
GEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGINGGVYLSDLEWVDATH
GDDDKSKTVQKDKPFTPGNNGSNNKIKLLIDGKEVEFNKGLGTVASNPSS
IKYDVSGANVTRFISYVGIDRSANHLNSDYADIQKFEVVADGKVIYSSDS
KYPKGIKYDTSAFLVDVEIPKDTQTIELKSYSGKHTWADELVLGGALFMA
N

Ligand information

• Ligand ID: GLA
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-PHYPRBDBSA-N
• SMILES:
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-galactopyranose;
  alpha-D-galactose;
  D-galactose;
  galactose;
  ALPHA D-GALACTOSE
• ChEMBL: CHEMBL1233058
• ZINC: ZINC000000901155
• PDB chain: 2ygm Chain C Residue 4

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ygm The Overall Architecture and Receptor Binding of Pneumococcal Carbohydrate Antigen Hydrolyzing Enzymes.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): D80 T94 N153 T215 W216 G217 E219
• Binding residue (residue number reindexed from 1): D19 T33 N92 T154 W155 G156 E158
• Annotation score: 4

External links

• PDB: RCSB:2ygm, PDBe:2ygm, PDBj:2ygm
• PDBsum: 2ygm
• PubMed: 21767550
• UniProt: C1CB04