Structure of PDB 6t2b Chain B Binding Site BS01
Receptor Information
>6t2b Chain B (length=439) Species:
239935
(Akkermansia muciniphila) [
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AVEIPAGDHLWKSAPRPSGSTYMGGFKAPRLGRIRLAFIGVGGRGFSHLA
QMCVMDGVEIVGICDLKEELTKRGVDRVLSRMGKSPLGYSGGDMEYLTML
KELKPDAVIISTDWSSHARIACDSMKHGAHAFVEVPLAVSLEELWSLVDT
SEATRKHCMMMENVNYGRDELMFLNMVRQGVIGDLLHGEAAYIHCLVTQL
GDTRGEGAWRPEYHTRINGNLYPTHGLGPVAQYMNLERGEDRFCRVAAFA
SPALGRNAYAKKHLPADHRWNNTPFICGDMNTAVVKTQLGRTILVQLDET
SPRPYSRANLIQGTEGTLAGFPTRVAGEKLGNGNYHEWIEGREKLAAIYE
KYDHPLWKRIGELATKMGGHGGMDFVMLSRIVECLRNGEPMDQNVYEGAS
WSSLLPLTARSIAQGGMPVEFPDFTRGDWKTTMPLAVVS
Ligand information
Ligand ID
NAD
InChI
InChI=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
InChIKey
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
Software
SMILES
CACTVS 3.341
NC(=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 1.5.0
c1cc(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 3.341
NC(=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 1.5.0
c1cc(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
Formula
C21 H27 N7 O14 P2
Name
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBL
CHEMBL1234613
DrugBank
DB14128
ZINC
PDB chain
6t2b Chain B Residue 502 [
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Receptor-Ligand Complex Structure
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PDB
6t2b
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
Resolution
2.13 Å
Binding residue
(original residue number in PDB)
G74 G77 R78 D99 L100 D127 S145 T146 W148 H151 E168 V169 N197 G239 E240 W243 Y256 H259 H404
Binding residue
(residue number reindexed from 1)
G40 G43 R44 D65 L66 D93 S111 T112 W114 H117 E134 V135 N163 G205 E206 W209 Y222 H225 H370
Annotation score
4
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
PDBsum
6t2b
PubMed
UniProt
B2UQL7
|G1092_AKKM8 Glycosyl hydrolase family 109 protein 2 (Gene Name=Amuc_0920)
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