1GDU Hydrolase date Sep 29, 2000
title Fusarium Oxysporum Trypsin At Atomic Resolution
authors W.R.Rypniewski, P.Oestergaard, M.Noerregaard-Madsen, M.Dauter, K
compound source
Molecule: Trypsin
Chain: A
Ec: 3.4.21.4
 Organism_scientific: Fusarium Oxysporum
Organism_taxid: 5507

Molecule: Gly-Ala-Arg
Chain: B
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.290 37.050 40.259 102.46 103.81 102.07
method X-Ray Diffractionresolution 1.07 Å
ligand SO4 enzyme Hydrolase E.C.3.4.21.4 BRENDA
related structures by homologous chain: 1PQ8, 1PQA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceFusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding., Rypniewski WR, Ostergaard PR, Norregaard-Madsen M, Dauter M, Wilson KS, Acta Crystallogr D Biol Crystallogr 2001 Jan;57(Pt 1):8-19. PMID:11134922
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (1gdu.pdb1.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 1GDU
  • CSU: Contacts of Structural Units for 1GDU
  • Likely Quarternary Molecular Structure file(s) for 1GDU
  • Structure Factors (685 Kb)
  • Retrieve 1GDU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GDU from S2C, [Save to disk]
  • Re-refined 1gdu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1GDU 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 1GDU
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1GDU 1GDUA 1GDUB from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1GDU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gdua_, region A [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: [1gdu] [1gdu_A] [1gdu_B]
  • SWISS-PROT database: [P35049]
  • Domain organization of [TRYP_FUSOX] by SWISSPFAM
  • Domain found in 1GDU: [Tryp_SPc ] by SMART
    • Other resources with information on 1GDU
  • Community annotation for 1GDU 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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