Structure of PDB 6rd1 Chain B Binding Site BS01

Receptor Information
>6rd1 Chain B (length=304) Species: 411470 (Mediterraneibacter gnavus ATCC 29149) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNLEKYKGVIPAFYACYDKEGNISPEGVQGLTKYFVKKGVKGVYVNGSSG
ECIYQSVEDRKIVLENVMKVAEGKLTVIAHVACNNTKDSQELARHAEGLG
VDAIAAIPPIYFHLPEYAIAQYWNAISAAAPNTDFVIYNIPQLAGVALTQ
NLFVEMRKNPNVIGVANSSMPVQDIQMFKQAAGAEYIIFNGPDEQFMSGR
VIGAEGAIGGTYGAMPELYLKLDECINAGKMTEARKIQYACNEIIYKMCS
AHGNMYAVIKAILKINEGLELGAVREPLPALVDEDMEIVKEAAQMICDAK
KKFL
Ligand information
Ligand IDSI3
InChIInChI=1S/C11H19NO9/c1-4(14)12-8(5(15)2-6(16)11(20)21)10(19)9(18)7(17)3-13/h5,7-10,13,15,17-19H,2-3H2,1H3,(H,12,14)(H,20,21)/t5-,7+,8+,9+,10+/m0/s1
InChIKeyKBGAYAKRZNYFFG-BOHATCBPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(=O)CC(O)C(NC(=O)C)C(O)C(O)C(O)CO
OpenEye OEToolkits 1.7.6CC(=O)N[C@H]([C@H](CC(=O)C(=O)O)O)[C@H]([C@@H]([C@@H](CO)O)O)O
CACTVS 3.370CC(=O)N[CH]([CH](O)CC(=O)C(O)=O)[CH](O)[CH](O)[CH](O)CO
OpenEye OEToolkits 1.7.6CC(=O)NC(C(CC(=O)C(=O)O)O)C(C(C(CO)O)O)O
CACTVS 3.370CC(=O)N[C@H]([C@@H](O)CC(=O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO
FormulaC11 H19 N O9
Name5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid;
N-acetylneuraminic acid, ketone form
ChEMBLCHEMBL2105945
DrugBankDB11797
ZINCZINC000004214715
PDB chain6rd1 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rd1 Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut.
Resolution1.892 Å
Binding residue
(original residue number in PDB)		Y45 G48 S49 S50 S169 G192 D194 E195 G210 G211
Binding residue
(residue number reindexed from 1)		Y44 G47 S48 S49 S168 G191 D193 E194 G209 G210
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) S49 Y112 Y139 L144 A167 I209
Catalytic site (residue number reindexed from 1) S48 Y111 Y138 L143 A166 I208
Enzyme Commision number 4.1.3.3: N-acetylneuraminate lyase.
Gene Ontology
Molecular Function
GO:0008747 N-acetylneuraminate lyase activity
GO:0016829 lyase activity
Biological Process
GO:0019262 N-acetylneuraminate catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6rd1, PDBe:6rd1, PDBj:6rd1
PDBsum6rd1
PubMed31636419
UniProtA7B555|NANA_MEDG7 N-acetylneuraminate lyase (Gene Name=nanA)

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