1EB1 Hydrolase Hydrolase Inhibitor date Jul 18, 2001
title Complex Structure Of Human Thrombin With N-Methyl-Arginine I
authors R.Friedrich, T.Steinmetzer, W.Bode
compound source
Molecule: Peptide Inhibitor
Chain: A
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Thrombin Heavy Chain
Chain: H

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood

Molecule: Thrombin Light Chain
Chain: L
Fragment: Catalytic Domain Residues 364-620
Ec: 3.4.21.5

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Blood

Molecule: 3-Cyclohexyl-D-Alanyl-L-Prolyl-N~2~-Methyl-L-Argi
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.191 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.839 71.508 71.710 90.00 99.34 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand MMO, ZAL enzyme Hydrolase E.C.3.4.21.5 BRENDA
related structures by homologous chain: 1QBV, 1TOM
Gene
Ontology
ChainFunctionProcessComponent
H


L


Primary referenceThe methyl group of N(alpha)(Me)Arg-containing peptides disturbs the active-site geometry of thrombin, impairing efficient cleavage., Friedrich R, Steinmetzer T, Huber R, Sturzebecher J, Bode W, J Mol Biol. 2002 Mar 1;316(4):869-74. PMID:11884127
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (1eb1.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 1EB1
  • CSU: Contacts of Structural Units for 1EB1
  • Likely Quarternary Molecular Structure file(s) for 1EB1
  • Retrieve 1EB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EB1 from S2C, [Save to disk]
  • View 1EB1 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 1EB1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1EB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n1eb1, region B:198-357 [Jmol] [rasmolscript] [script source]
        - Domain d1q1eb1, region B:236-370 [Jmol] [rasmolscript] [script source]
        - Domain d1eb1.1, 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: [1eb1_H] [1eb1_B] [1eb1_A] [1eb1_L] [1eb1]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1EB1: [Tryp_SPc ] by SMART
  • Other resources with information on 1EB1
  • Community annotation for 1EB1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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