Structure of PDB 4q6o Chain A Binding Site BS04

Receptor Information

>4q6o Chain A (length=417) Species: 85962 (Helicobacter pylori 26695)

MIEKAPTNVEDRDKAPHLLLLAGIQGDEPGGFNATNLFLMHYSVLKGLVE
VVPVLNKPSMLRNHRGLYGDMNRKFAALDKNDPEYPTIQEIKSLIAKPSI
DAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLAFA
NNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAFAN
EASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFDLNPNSVHALINDKNL
WAKISSLPKMPLFNLRPKLNHFPLPHNTKIPQIPIESNAYIVGLVKNKQE
VFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKESF
YIHAMDNIRANVIGFSVSNENKPNEAGYTIKFKDFQKRFSLDKQERIYRI
EFYKNNAFSGMILVKFV

Ligand information

• Ligand ID: API
• InChI: InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
• InChIKey: GMKMEZVLHJARHF-SYDPRGILSA-N
• SMILES:
  CACTVS 3.370: N[CH](CCC[CH](N)C(O)=O)C(O)=O
  OpenEye OEToolkits 1.7.2: C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
  OpenEye OEToolkits 1.7.2: C(CC(C(=O)O)N)CC(C(=O)O)N
  CACTVS 3.370: N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
  ACDLabs 12.01: O=C(O)C(N)CCCC(C(=O)O)N
• Formula: C7 H14 N2 O4
• Name: 2,6-DIAMINOPIMELIC ACID
• ChEMBL: CHEMBL415306
• ZINC: ZINC000001532722
• PDB chain: 4q6o Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4q6o Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape
• Resolution: 1.41 Å
• Binding residue (original residue number in PDB): N93 R94 H126 H128 W148 M203 T208 A220 E222
• Binding residue (residue number reindexed from 1): N72 R73 H105 H107 W127 M182 T187 A199 E201
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:4q6o, PDBe:4q6o, PDBj:4q6o
• PDBsum: 4q6o
• PubMed: 25372672
• UniProt: O25708