Structure of PDB 2b5t Chain B Binding Site BS02

Receptor Information

>2b5t Chain B (length=252) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE

Ligand information

• Ligand ID: GU6
• InChI: InChI=1S/C6H12O15S3/c7-3-2(1-18-22(9,10)11)19-6(8)5(21-24(15,16)17)4(3)20-23(12,13)14/h2-8H,1H2,(H,9,10,11)(H,12,13,14)(H,15,16,17)/t2-,3-,4+,5-,6+/m1/s1
• InChIKey: GRHWGVDHRAZFMQ-DVKNGEFBSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OS(=O)(=O)O)OS(=O)(=O)O)O)OS(=O)(=O)O
  CACTVS 3.385: O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O[S](O)(=O)=O)[C@H]1O[S](O)(=O)=O
  ACDLabs 12.01: C1(C(C(OS(=O)(O)=O)C(O)C(COS(=O)(O)=O)O1)OS(O)(=O)=O)O
  CACTVS 3.385: O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O[S](O)(=O)=O)[CH]1O[S](O)(=O)=O
  OpenEye OEToolkits 1.7.6: C(C1C(C(C(C(O1)O)OS(=O)(=O)O)OS(=O)(=O)O)O)OS(=O)(=O)O
• Formula: C6 H12 O15 S3
• Name: 2,3,6-tri-O-sulfo-alpha-D-glucopyranose;
  2,3,6-TRI-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE;
  2,3,6-tri-O-sulfo-alpha-D-glucose;
  2,3,6-tri-O-sulfo-D-glucose;
  2,3,6-tri-O-sulfo-glucose
• ZINC: ZINC000136252347
• PDB chain: 2b5t Chain G Residue 15

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2b5t Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): H91 K236
• Binding residue (residue number reindexed from 1): H87 K241
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D102 E192 G193 D194 A195 G196
• Catalytic site (residue number reindexed from 1): H43 D99 E195 G196 D197 A198 G199
• 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

External links

• PDB: RCSB:2b5t, PDBe:2b5t, PDBj:2b5t
• PDBsum: 2b5t
• PubMed: 16973611
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)