Structure of PDB 2fuq Chain B Binding Site BS01

Receptor Information

>2fuq Chain B (length=747) Species: 984 (Pedobacter heparinus)

QTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWA
DMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGR
EAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTR
FVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPE
MYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRM
GAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLA
GSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSG
SPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAID
AGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTD
FAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTY
LKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKF
WLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKG
KDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIAD
NTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTF
KFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR

Ligand information

• Ligand ID: RAM
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-HGVZOGFYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-rhamnopyranose;
  alpha-L-rhamnose;
  6-deoxy-alpha-L-mannopyranose;
  L-rhamnose;
  rhamnose
• ZINC: ZINC000003861280
• PDB chain: 2fuq Chain D Residue 4

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2fuq Crystal Structure of Heparinase II from Pedobacter heparinus and Its Complex with a Disaccharide Product.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): K102 T105
• Binding residue (residue number reindexed from 1): K77 T80
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 4.2.2.7: heparin lyase.
  4.2.2.8: heparin-sulfate lyase.

Gene Ontology

Molecular Function

• GO:0008201 heparin binding
• GO:0015021 heparin-sulfate lyase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0047488 heparin lyase activity

Biological Process

• GO:0030211 heparin catabolic process

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:2fuq, PDBe:2fuq, PDBj:2fuq
• PDBsum: 2fuq
• PubMed: 16565082
• UniProt: C6XZB6|HEPB_PEDHD Heparin and heparin-sulfate lyase (Gene Name=hepB)