Structure of PDB 6gh2 Chain B Binding Site BS01

Receptor Information
>6gh2 Chain B (length=905) Species: 856729 (Paenibacillus sp. YM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KGWKFQGEQGEFRLEQPEHNSYLYFPLVNEAGMMSAVTPNLHGEITSGHN
TFLMEPVSAESLHNSKASRNFWVFIEGYGAWSVSGNSARQNAARFTGEEE
RSAVEAGFLWHAVTRENEKAGLKARTVSFVPVTDDKIELMRVTLTNTGNA
PLKLTPTAAIPLYGRSADDLRDHRHVTSLLHRIFTSEYGIEVQPALSFDE
RGHRVNKVTYGVFGAEAGGTAPAGFFPVTEDFIGEGGALDWPEAVVANRE
PDAQAGTAVEGYEAVGALRFAPVELAPGKSVSYVVAMVISGDRIDVGRYA
ADYLAAGRFDALLEQNRAYWRDKLDTVRFSSGDGEQDLWMKWVTLQPILR
RLYGNSFLPYHDYGRGGRGWRDLWQDCLALMVMEPAEVRHLLLNNYAGVR
MDGSNATIIGAGPGEFVADRNNIPRVWMDHGAWPLMTTLLYLHQSGDLDL
LFQPQSYFRDVFVKRCRERDASWTPEQGNKLLTADGQIYEGTILEHILLQ
NIVPFFNVGEHGNIKLEGADWNDGLDLAPERGESVAFTAFYASNLMELSE
LLLELQKRTGKDSLDIAEEMALLLDTLGKPISYDSIQEKRSLLDRYYDAV
TPRVSGKKLLLDIRKVAEDLKRKADWAVAHLRGSEWIQSKEGYAWFNGYY
NNDGERVEGDHPDGVRMTLTGQVFAIMGGVATDEQTEKISQAVNRYLKDE
RIGYRLNSRFGGIQQNLGRAFGFAFGHKENGAMFSHMTVMYANALYKRGF
VQEGFEVLDSIYRLSADFENSRIYPGVPEYINERGRGMYTYLTGSASWLL
LTQLTEVYGVKGRFGDLRLEPKLVQAQFDGSGEAAVETLFAGRMLRVVYR
NPQAAEHGQYRVDSVSLNGQSVDCQNDGAGCLIGRSLIEALPADGVHELI
VTLGR
Ligand information
Ligand IDG1P
InChIInChI=1S/C6H13O9P/c7-1-2-3(8)4(9)5(10)6(14-2)15-16(11,12)13/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5-,6-/m1/s1
InChIKeyHXXFSFRBOHSIMQ-VFUOTHLCSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[CH]1O[CH](O[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
ACDLabs 12.01O=P(O)(OC1OC(C(O)C(O)C1O)CO)O
OpenEye OEToolkits 1.7.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)O)O
CACTVS 3.370OC[C@H]1O[C@H](O[P](O)(O)=O)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.7.0C(C1C(C(C(C(O1)OP(=O)(O)O)O)O)O)O
FormulaC6 H13 O9 P
Name1-O-phosphono-alpha-D-glucopyranose;
ALPHA-D-GLUCOSE-1-PHOSPHATE;
1-O-phosphono-alpha-D-glucose;
1-O-phosphono-D-glucose;
1-O-phosphono-glucose
ChEMBL
DrugBankDB02843
ZINCZINC000004073375
PDB chain6gh2 Chain B Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6gh2 Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		R353 R374 W524 D526 E732 F737 E782 T796 G797
Binding residue
(residue number reindexed from 1)		R350 R371 W521 D523 E729 F734 E779 T793 G794
Annotation score5
Enzymatic activity
Enzyme Commision number 2.4.1.31: laminaribiose phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016757 glycosyltransferase activity
GO:0030246 carbohydrate binding
GO:0050045 laminaribiose phosphorylase activity
Biological Process
GO:0005975 carbohydrate metabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:6gh2, PDBe:6gh2, PDBj:6gh2
PDBsum6gh2
PubMed29856496
UniProtD7UT17

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