Structure of PDB 6gh3 Chain B Binding Site BS01

Receptor Information
>6gh3 Chain B (length=899) 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
MDGSNATIIGAGPGEFVADRPRVWMDHGAWPLMTTLLYLHQSGDLDLLFQ
PQSYFRDVFVKRCRERDASWTPEQGNKLLTADGQIYEGTILEHILLQNIV
PFFNVGEHGNIKLEGADWNDGLDLAPERGESVAFTAFYASNLMELSELLL
ELQKRTGKDSLDIAEEMALLLDTLGKPISYDSIQEKRSLLDRYYDAVTPR
VSGKKLLLDIRKVAEDLKRKADWAVAHLRGSEWIQSKEGYAWFNGYYNND
GERVEGDHPDGVRMTLTGQVFAIMGGVATDEQTEKISQAVNRYLKDERIG
YRLNSRFGGIQQNLGRAFGFAFGHKENGAMFSHMTVMYANALYKRGFVQE
GFEVLDSIYRLSADFENSRIYPGVPEYINERGRGMYTYLTGSASWLLLTQ
LTEVYGVKGRFGDLRLEPKLVQAQFDGSGEAAVETLFAGRMLRVVYRNPQ
AAEHGQYRVDSVSLNGQSVDCQAGCLIGRSLIEALPADGVHELIVTLGR
Ligand information
Ligand IDM1P
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-RWOPYEJCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH](O[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O[P](O)(O)=O)[C@@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)OP(=O)(O)O)O)O)O)O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)OP(=O)(O)O)O)O)O)O
FormulaC6 H13 O9 P
Name1-O-phosphono-alpha-D-mannopyranose;
ALPHA-D-MANNOSE 1-PHOSPHATE;
1-O-phosphono-alpha-D-mannose;
1-O-phosphono-D-mannose;
1-O-phosphono-mannose
ChEMBLCHEMBL291890
DrugBankDB17678
ZINCZINC000004095569
PDB chain6gh3 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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PDB6gh3 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.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		R374 W524 E732 F737 E782 T796 G797
Binding residue
(residue number reindexed from 1)		R371 W518 E726 F731 E776 T790 G791
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:6gh3, PDBe:6gh3, PDBj:6gh3
PDBsum6gh3
PubMed29856496
UniProtD7UT17

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