1GZL Glycoprotein date May 23, 2002
title Crystal Structure Of C14linkmidiqn17: A Cross-Linked Inhibi Hiv-1 Entry Bound To The Gp41 Hydrophobic Pocket
authors S.K.Sia, P.A.Carr, A.G.Cochran, V.M.Malashkevich, P.S.Kim
compound source
Molecule: Fusion Protein Between The Hydrophobic Pocket Of And General Control Protein Gcn4-Piqi;
Chain: A, B
Fragment: Gp41 Hydrophobic Pocket, Residues 565-581, Gcn4, 249-276;
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae, Human Immunodeficiency Virus 1;
Organism_common: Baker'S Yeast, Hiv-1
Organism_taxid: 4932, 11676
Other_details: This Peptide Was Chemically Synthesized

Molecule: Envelope Glycoprotein Gp41
Chain: C, D
Fragment: Residues 628-639
Synonym: C14linkmid
Engineered: Yes
Mutation: Yes
Other_details: Sequence Of The Hiv-1 Gp41 Was Mutated At Me Asn 636 To Glutamate, And Their Side-Chains Cross-Linked Vi Diaminopentane Group

Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus
Organism_common: Hiv-1
Organism_taxid: 12721
Other_details: This Peptide Was Chemically Synthesized
symmetry Space Group: P 63
R_factor 0.208 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.358 38.358 169.695 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand ACE, CL, N2P enzyme
related structures by homologous chain: 1PIQ, 1ZIK
Primary referenceShort constrained peptides that inhibit HIV-1 entry., Sia SK, Carr PA, Cochran AG, Malashkevich VN, Kim PS, Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14664-9. Epub 2002 Nov 4. PMID:12417739
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (28 Kb) [Save to disk]
  • Biological Unit Coordinates (1gzl.pdb1.gz) 34 Kb
  • Biological Unit Coordinates (1gzl.pdb2.gz) 34 Kb
  • LPC: Ligand-Protein Contacts for 1GZL
  • CSU: Contacts of Structural Units for 1GZL
  • Likely Quarternary Molecular Structure file(s) for 1GZL
  • Structure Factors (69 Kb)
  • Retrieve 1GZL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GZL from S2C, [Save to disk]
  • Re-refined 1gzl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GZL 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 1GZL
  • 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 1GZL, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gzl.1, region A:,C [Jmol] [rasmolscript] [script source]
        - Domain d1gzl.2, region B:,D [Jmol] [rasmolscript] [script source]
  • Fold representative 1gzl 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: [1gzl_B] [1gzl] [1gzl_A] [1gzl_C] [1gzl_D]
  • SWISS-PROT database: [P04578] [P03069]
  • Belongs to the human immunodeficiency virus type 1 (hiv-1) fusion peptide (hiv-fp) family according to TCDB.
  • Domain organization of [ENV_HV1H2] [GCN4_YEAST] by SWISSPFAM
  • Other resources with information on 1GZL
  • Community annotation for 1GZL 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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