Structure of PDB 1lxm Chain A Binding Site BS02

Receptor Information
>1lxm Chain A (length=794) Species: 1311 (Streptococcus agalactiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HPQPVTTQIEKSVNTALNKNYVFNKADYQYTLTNPSLGKIVGGILYPNAT
GSTTVKISDKSGKIIKEVPLSVTASTEDNFTKLLDKWNDVTIGNYVYDTN
DSNMQKLNQKLDETNAKNIEAIKLDSNRTFLWKDLDNLNNSAQLTATYRR
LEDLAKQITNPHSTIYKNEKAIRTVKESLAWLHQNFYNVNKDIEGSANWW
DFEIGVPRSITGTLSLMNNYFTDAEIKTYTDPIEHFVPDAEYFRKTLVNP
FKALGGNLVDMGRVKIIEGLLRKDNTIIEKTSHSLKNLFTTATKAEGFYA
DGSYIDHTNVAYTGAYGNVLIDGLTQLLPIIQETDYKISNQELDMVYKWI
NQSFLPLIVKGELMDMSRGRSISREAASSHAAAVEVLRGFLRLANMSNEE
RNLDLKSTIKTIITSNKFYNVFNNLKSYSDIANMNKLLNDSTVATKPLKS
NLSTFNSMDRLAYYNAKKDFGFALSLHSKRTLNYEGMNDENTRGWYTGDG
MFYIYNSDQSHYSNHFWPTVNPYKMAGTTEKDAKREDTTKEAKEKTGQVT
GTSDFVGSVKLNDHFALAAMDFTNWDRTLTAQKGWVILNDKIVFLGSNIK
NTNGIGNVSTTIDQRKDDSKTPYTTYVNGKTISQQFTDTKSVFLESKEPG
RNIGYIFFKNSTIDIERKEQTGTWNSINRTSKNTSIVSNPFITISQKHDS
YGYMMVPNIDRTSFDKLANSKEVELLENSSKQQVIYDKNSQTWAVIKHDN
QESLINNQFKMNKAGLYLVQKVGNDYQNVYYQPQTMTKTDQLAI
Ligand information
Ligand IDBDP
InChIInChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2-,3+,4-,6+/m0/s1
InChIKeyAEMOLEFTQBMNLQ-QIUUJYRFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0[C@@H]1([C@@H]([C@H](O[C@H]([C@@H]1O)O)C(=O)O)O)O
OpenEye OEToolkits 1.7.0C1(C(C(OC(C1O)O)C(=O)O)O)O
CACTVS 3.370O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O
ACDLabs 12.01O=C(O)C1OC(O)C(O)C(O)C1O
CACTVS 3.370O[C@@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O
FormulaC6 H10 O7
Namebeta-D-glucopyranuronic acid;
beta-D-glucuronic acid;
D-glucuronic acid;
glucuronic acid
ChEMBLCHEMBL1159524
DrugBankDB03156
ZINCZINC000004097543
PDB chain1lxm Chain B Residue 6 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1lxm Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R560 N596 K598
Binding residue
(residue number reindexed from 1)		R388 N424 K426
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N429 H479 Y488 R542 E657
Catalytic site (residue number reindexed from 1) N257 H307 Y316 R370 E485
Enzyme Commision number 4.2.2.1: hyaluronate lyase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0030246 carbohydrate binding
Biological Process
GO:0005975 carbohydrate metabolic process
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1lxm, PDBe:1lxm, PDBj:1lxm
PDBsum1lxm
PubMed12130645
UniProtQ53591|HYSA_STRA3 Hyaluronate lyase (Gene Name=hylB)

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