Structure of PDB 6t2b Chain C Binding Site BS01

Receptor Information
>6t2b Chain C (length=436) Species: 239935 (Akkermansia muciniphila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPAGDHLWKSAPRPSGSTYMGGFKAPRLGRIRLAFIGVGGRGFSHLAQMC
VMDGVEIVGICDLKEELTKRGVDRVLSRMGKSPLGYSGGDMEYLTMLKEL
KPDAVIISTDWSSHARIACDSMKHGAHAFVEVPLAVSLEELWSLVDTSEA
TRKHCMMMENVNYGRDELMFLNMVRQGVIGDLLHGEAAYIHCLVTQLGDT
RGEGAWRPEYHTRINGNLYPTHGLGPVAQYMNLERGEDRFCRVAAFASPA
LGRNAYAKKHLPADHRWNNTPFICGDMNTAVVKTQLGRTILVQLDETSPR
PYSRANLIQGTEGTLAGFPTRVAGEKLGNGNYHEWIEGREKLAAIYEKYD
HPLWKRIGELATKMGGHGGMDFVMLSRIVECLRNGEPMDQNVYEGASWSS
LLPLTARSIAQGGMPVEFPDFTRGDWKTTMPLAVVS
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain6t2b Chain C Residue 502 [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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PDB6t2b The Catalytic Acid-Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable alpha-Retaining and beta-Inverting Activity in an N-Acetylgalactosaminidase from Akkermansia muciniphila
Resolution2.13 Å
Binding residue
(original residue number in PDB)		G77 R78 D99 L100 D127 S145 T146 W148 H151 E168 V169 N197 E240 W243 Y256 H259 H404
Binding residue
(residue number reindexed from 1)		G40 R41 D62 L63 D90 S108 T109 W111 H114 E131 V132 N160 E203 W206 Y219 H222 H367
Annotation score4
Enzymatic activity
Enzyme Commision number 3.2.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding

View graph for
Molecular Function
External links
PDB RCSB:6t2b, PDBe:6t2b, PDBj:6t2b
PDBsum6t2b
PubMed
UniProtB2UQL7|G1092_AKKM8 Glycosyl hydrolase family 109 protein 2 (Gene Name=Amuc_0920)

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