Structure of PDB 3e80 Chain A Binding Site BS01

Receptor Information
>3e80 Chain A (length=747) Species: 984 (Pedobacter heparinus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWA
DMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGR
EAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTR
FVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPE
MYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRM
GAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLA
GSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSG
SPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAID
AGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTD
FAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTY
LKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKF
WLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKG
KDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIAD
NTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTF
KFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR
Ligand information
Ligand IDGCD
InChIInChI=1S/C6H8O6/c7-2-1-3(5(9)10)12-6(11)4(2)8/h1-2,4,6-8,11H,(H,9,10)/t2-,4+,6+/m0/s1
InChIKeyIAKKJSVSFCTLRY-YKKSOZKNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=C(OC(C(C1O)O)O)C(=O)O
CACTVS 3.370O[C@@H]1OC(=C[C@H](O)[C@H]1O)C(O)=O
CACTVS 3.370O[CH]1OC(=C[CH](O)[CH]1O)C(O)=O
OpenEye OEToolkits 1.7.6C1=C(O[C@H]([C@@H]([C@H]1O)O)O)C(=O)O
ACDLabs 12.01O=C(O)C=1OC(O)C(O)C(O)C=1
FormulaC6 H8 O6
Name4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid;
4,5-DEHYDRO-D-GLUCURONIC ACID;
4-deoxy-alpha-L-threo-hex-4-enuronic acid;
4-deoxy-L-threo-hex-4-enuronic acid;
4-deoxy-threo-hex-4-enuronic acid
ChEMBL
DrugBankDB02305
ZINC
PDB chain3e80 Chain G Residue 2 [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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PDB3e80 Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		D145 H202 E205 Y257 H406 Y429
Binding residue
(residue number reindexed from 1)		D120 H177 E180 Y232 H381 Y404
Annotation score4
Enzymatic activity
Enzyme Commision number 4.2.2.7: heparin lyase.
4.2.2.8: heparin-sulfate lyase.
Gene Ontology

View graph for
Molecular Function
External links
PDB RCSB:3e80, PDBe:3e80, PDBj:3e80
PDBsum3e80
PubMed20404324
UniProtC6XZB6|HEPB_PEDHD Heparin and heparin-sulfate lyase (Gene Name=hepB)

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