1GHY Hydrolase Hydrolase Inhibitor date Jan 22, 2001
title A Novel Serine Protease Inhibition Motif Involving A Multi-C Short Hydrogen Bonding Network At The Active Site
authors B.A.Katz, K.Elrod, C.Luong, M.Rice, R.L.Mackman, P.A.Sprengeler, J J.Hatayte, J.Janc, J.Link, J.Litvak, R.Rai, K.Rice, S.Sideris, E.V W.Young
compound source
Molecule: Thrombin
Chain: L
Fragment: Light Chain, Residues 328-363
Synonym: Coagulation Factor II
Ec: 3.4.21.5
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Thrombin
Chain: H
Fragment: Heavy Chain, Residues 364-620
Synonym: Coagulation Factor II
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Acetyl Hirudin
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Hirudo Medicinalis
Organism_taxid: 6421
symmetry Space Group: C 1 2 1
R_factor 0.195 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.890 72.220 72.740 90.00 100.97 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand 121, CA, NA, TYS, ZN BindingDB enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1GHV, 1XMN
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceA novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site., Katz BA, Elrod K, Luong C, Rice MJ, Mackman RL, Sprengeler PA, Spencer J, Hataye J, Janc J, Link J, Litvak J, Rai R, Rice K, Sideris S, Verner E, Young W, J Mol Biol 2001 Apr 13;307(5):1451-86. PMID:11292354
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (1ghy.pdb1.gz) 118 Kb
  • Biological Unit Coordinates (1ghy.pdb2.gz) 235 Kb
  • LPC: Ligand-Protein Contacts for 1GHY
  • CSU: Contacts of Structural Units for 1GHY
  • Likely Quarternary Molecular Structure file(s) for 1GHY
  • Structure Factors (173 Kb)
  • Retrieve 1GHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GHY from S2C, [Save to disk]
  • Re-refined 1ghy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GHY in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1GHY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1GHY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ghy.1, region L:,H [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ghy_L] [1ghy_I] [1ghy_H] [1ghy]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1GHY: [Tryp_SPc ] by SMART
  • Other resources with information on 1GHY
  • Community annotation for 1GHY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1GHY from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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