1DVA Hydrolase Hydrolase Inhibitor date Jan 20, 2000
title Crystal Structure Of The Complex Between The Peptide Exosite E-76 And Coagulation Factor Viia
authors C.Eigenbrot, M.H.Ultsch
compound source
Molecule: Des-Gla Factor Viia (Heavy Chain)
Chain: H, I
Ec: 3.4.21.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Human Kidney Cell Line 293
Expression_system_plasmid: Pcmv5

Molecule: Des-Gla Factor Viia (Light Chain)
Chain: L, M
Ec: 3.4.21.21
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Human Kidney Cell Line 293
Expression_system_plasmid: Pcmv5

Molecule: Peptide E-76
Chain: X, Y
Engineered: Yes

Synthetic: Yes
Other_details: Peptide E-76 Was Synthesized On A Solid Supp Cleaved And Purified
symmetry Space Group: P 1 21 1
R_factor 0.225 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.490 55.260 111.730 90.00 99.48 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand 0Z6, ACE, BGC, CA, CAC, CH2, DPN, FUC, FUL, GAL, GLC enzyme Hydrolase E.C.3.4.21.21 BRENDA
related structures by homologous chain: 1FFM, 1J9C
Primary referencePeptide exosite inhibitors of factor VIIa as anticoagulants., Dennis MS, Eigenbrot C, Skelton NJ, Ultsch MH, Santell L, Dwyer MA, O'Connell MP, Lazarus RA, Nature 2000 Mar 30;404(6777):465-70. PMID:10761907
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (1dva.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (1dva.pdb2.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 1DVA
  • CSU: Contacts of Structural Units for 1DVA
  • Likely Quarternary Molecular Structure file(s) for 1DVA
  • Retrieve 1DVA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DVA from S2C, [Save to disk]
  • View 1DVA 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 1DVA
  • 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 1DVA, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dvah_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1dvai_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1dval1, region L:42-86 [Jmol] [rasmolscript] [script source]
        - Domain d1dval2, region L:87-142 [Jmol] [rasmolscript] [script source]
        - Domain d1dvam1, region M:42-86 [Jmol] [rasmolscript] [script source]
        - Domain d1dvam2, region M:87-142 [Jmol] [rasmolscript] [script source]
  • Fold representative 1dva 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: [1dva_M] [1dva_H] [1dva_C] [1dva_I] [1dva_X] [1dva] [1dva_Y] [1dva_L] [1dva_D]
  • SWISS-PROT database: [P08709]
  • Domain organization of [FA7_HUMAN] by SWISSPFAM
  • Domains found in 1DVA: [EGF] [EGF_CA] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 1DVA with the sequences similar proteins can be viewed for 1DVA's classification [FA7_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [FA7_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DVA
  • Community annotation for 1DVA at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1DVA from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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