1KJ4 Hydrolase date Dec 04, 2001
title Substrate Shape Determines Specificity Of Recognition Recognition For Hiv-1 Protease: Analysis Of Crystal Structures Of Six Substrate Complexes
authors C.A.Schiffer
compound source
Molecule: Pol Polyprotein
Chain: A, B, C, D
Fragment: Hiv-1 Protease, Residues 57-155
Ec: 3.4.23.16
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Gag Polyprotein
Chain: P, S
Fragment: Matrix-Capsid Substrate Peptide, Residues 127- 136;
Engineered: Yes

Synthetic: Yes
symmetry Space Group: I 2 2 2
R_factor 0.197 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.651 93.808 118.172 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand ACT enzyme Hydrolase E.C.3.4.23.16 BRENDA
related structures by homologous chain: 1MUI, 2UPJ
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceSubstrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes., Prabu-Jeyabalan M, Nalivaika E, Schiffer CA, Structure (Camb) 2002 Mar;10(3):369-81. PMID:12005435
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1kj4.pdb1.gz) 34 Kb
  • Biological Unit Coordinates (1kj4.pdb2.gz) 33 Kb
  • Biological Unit Coordinates (1kj4.pdb3.gz) 254 Kb
  • LPC: Ligand-Protein Contacts for 1KJ4
  • CSU: Contacts of Structural Units for 1KJ4
  • Likely Quarternary Molecular Structure file(s) for 1KJ4
  • Retrieve 1KJ4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KJ4 from S2C, [Save to disk]
  • View 1KJ4 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 1KJ4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KJ4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kj4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kj4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1kj4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1kj4d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1kj4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1kj4_S] [1kj4_B] [1kj4_A] [1kj4_C] [1kj4_P] [1kj4] [1kj4_D]
  • SWISS-PROT database: [P20873] [P03369] [P20875]
  • Domain organization of [GAG_HV1JR] [POL_HV1A2] [POL_HV1JR] by SWISSPFAM
  • Other resources with information on 1KJ4
  • Community annotation for 1KJ4 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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