Structure of PDB 3pma Chain D Binding Site BS04

Receptor Information
>3pma Chain D (length=259) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDI
ALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTT
SVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDA
CEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDRLGS
Ligand information
Ligand IDGU4
InChIInChI=1S/C6H12O18S4/c7-6-5(24-28(17,18)19)4(23-27(14,15)16)3(22-26(11,12)13)2(21-6)1-20-25(8,9)10/h2-7H,1H2,(H,8,9,10)(H,11,12,13)(H,14,15,16)(H,17,18,19)/t2-,3-,4+,5-,6+/m1/s1
InChIKeySPIXVQOXHJQNTH-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C(C1C(C(C(C(O1)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O
ACDLabs 12.01OC1OC(COS(=O)(=O)O)C(OS(=O)(=O)O)C(OS(=O)(O)=O)C1OS(=O)(=O)O
OpenEye OEToolkits 2.0.7C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O
CACTVS 3.385O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O[S](O)(=O)=O)[CH](O[S](O)(=O)=O)[CH]1O[S](O)(=O)=O
CACTVS 3.385O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O[S](O)(=O)=O)[C@H](O[S](O)(=O)=O)[C@H]1O[S](O)(=O)=O
FormulaC6 H12 O18 S4
Name2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose;
2,3,4,6-tetra-O-sulfonato-alpha-D-glucose;
2,3,4,6-tetra-O-sulfonato-D-glucose;
2,3,4,6-tetra-O-sulfonato-glucose
ChEMBL
DrugBank
ZINCZINC000058632064
PDB chain3pma Chain F Residue 1 [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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PDB3pma Interaction of thrombin with sucrose octasulfate.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H91 K236 W237 K240
Binding residue
(residue number reindexed from 1)		H87 K248 W249 K252
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E202 G203 D204 S205 G206
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3pma, PDBe:3pma, PDBj:3pma
PDBsum3pma
PubMed21736375
UniProtP00735|THRB_BOVIN Prothrombin (Gene Name=F2)

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