Structure of PDB 5g5k Chain A Binding Site BS01

Receptor Information
>5g5k Chain A (length=333) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMQGSLMLDIGGTWLTAEDRQILRHPEVGGLIIFARNIEHPAQVRELCAA
IRAIRPDLLLAVDQEGGRVQRLRQGFVRLPAMRAIADNPNAEELAEHCGW
LMATEVQAVGLDLSFAPVLDLDHQRSAVVGSRAFEGDPERAALLAGAFIR
GMHAAGMAATGKHFPGHGWAEADSHVAIPEDARSLEEIRRSDLVPFARLA
GQLDALMPAHVIYPQVDPQPAGFSRRWLQEILRGELKFDGVIFSDDLSMA
GAHVVGDAASRIEAALAAGCDMGLVCNDRASAELALAALQRLKVTPPSRL
QRMRGKGYANTDYRQQPRWLEALSALRAAQLID
Ligand information
Ligand IDNOK
InChIInChI=1S/C8H16N2O4/c1-4(12)10-5-2-9-6(3-11)8(14)7(5)13/h5-9,11,13-14H,2-3H2,1H3,(H,10,12)/t5-,6+,7+,8+/m0/s1
InChIKeyGBRAQQUMMCVTAV-LXGUWJNJSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1CN[CH](CO)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0CC(=O)NC1CNC(C(C1O)O)CO
CACTVS 3.341CC(=O)N[C@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0CC(=O)N[C@H]1CN[C@@H]([C@H]([C@@H]1O)O)CO
ACDLabs 10.04O=C(NC1C(O)C(O)C(NC1)CO)C
FormulaC8 H16 N2 O4
Name2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
ChEMBLCHEMBL382689
DrugBank
ZINCZINC000005167384
PDB chain5g5k Chain A Residue 1333 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5g5k Catalytic Cycle of the N-Acetylglucosaminidase NagZ from Pseudomonas aeruginosa.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D62 R131 H162 D244
Binding residue
(residue number reindexed from 1)		D63 R132 H163 D245
Annotation score1
Binding affinityBindingDB: Ki=300nM
Enzymatic activity
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0009254 peptidoglycan turnover
GO:0046677 response to antibiotic
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5g5k, PDBe:5g5k, PDBj:5g5k
PDBsum5g5k
PubMed28482153
UniProtQ9HZK0|NAGZ_PSEAE Beta-hexosaminidase (Gene Name=nagZ)

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