1V6D Hydrolase date Nov 28, 2003
title The Crystal Structure Of The Trypsin Complex With Synthetic Heterochiral Peptide
authors N.Shamaladevi, V.Pattabhi
compound source
Molecule: Trypsin
Chain: A
Ec: 3.4.21.4
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Pd(Aib)L(Aib)La
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: A Heterochiral Heptapeptide Synthesized Chem
symmetry Space Group: P 21 21 21
R_factor 0.153 R_Free 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.930 53.719 77.473 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACT, AIB, CA, NME, TBF enzyme Hydrolase E.C.3.4.21.4 BRENDA
related structures by homologous chain: 1H9I, 1ZZZ
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSecondary binding site of trypsin: revealed by crystal structure of trypsin-Peptide complex., Shamaladevi N, Pattabhi V, J Biomol Struct Dyn 2005 Jun;22(6):635-42. PMID:15842169
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (1v6d.pdb1.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 1V6D
  • CSU: Contacts of Structural Units for 1V6D
  • Likely Quarternary Molecular Structure file(s) for 1V6D
  • Structure Factors (110 Kb)
  • Retrieve 1V6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V6D from S2C, [Save to disk]
  • Re-refined 1v6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V6D 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 1V6D
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1V6D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v6da_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1v6d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1v6d_A] [1v6d] [1v6d_B]
  • SWISS-PROT database: [P00761]
  • Domain organization of [TRYP_PIG] by SWISSPFAM
  • Domain found in 1V6D: [Tryp_SPc ] by SMART
  • Other resources with information on 1V6D
  • Community annotation for 1V6D 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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