3F6U Hydrolase Hydrolase Inhibitor date Nov 06, 2008
title Crystal Structure Of Human Activated Protein C (Apc) Complex Ppack
authors A.E.Schmidt, K.Padmanabhan, M.C.Underwood, W.Bode, T.Mather, S.P.
compound source
Molecule: Vitamin K-Dependent Protein C Heavy Chain
Chain: H
Fragment: Unp Residues 212-451
Synonym: Autoprothrombin Iia, Anticoagulant Protein C, Bloo Coagulation Factor Xiv;
Ec: 3.4.21.69
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Vitamin K-Dependent Protein C Light Chain
Chain: L
Fragment: Unp Residues 91-188
Synonym: Autoprothrombin Iia, Anticoagulant Protein C, Bloo Coagulation Factor Xiv;
Ec: 3.4.21.69

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.161 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.060 89.600 101.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 0G6, ACL, CA, DPN, NA enzyme Hydrolase E.C.3.4.21.69 BRENDA
Primary referenceThermodynamic linkage between the S1 site, the Na+ site, and the Ca2+ site in the protease domain of human activated protein C (APC). Sodium ion in the APC crystal structure is coordinated to four carbonyl groups from two separate loops., Schmidt AE, Padmanabhan K, Underwood MC, Bode W, Mather T, Bajaj SP, J Biol Chem. 2002 Aug 9;277(32):28987-95. Epub 2002 May 23. PMID:12029084
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (3f6u.pdb1.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 3F6U
  • CSU: Contacts of Structural Units for 3F6U
  • Likely Quarternary Molecular Structure file(s) for 3F6U
  • Structure Factors (188 Kb)
  • Retrieve 3F6U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F6U from S2C, [Save to disk]
  • Re-refined 3f6u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F6U 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 3F6U
  • 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 3F6U, from MSDmotif at EBI
  • Fold representative 3f6u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f6u_L] [3f6u] [3f6u_H] [3f6u_I]
  • SWISS-PROT database: [P04070]
  • Domain organization of [PROC_HUMAN] by SWISSPFAM
  • Domains found in 3F6U: [EGF] [Tryp_SPc ] by SMART
  • Alignments of the sequence of 3F6U with the sequences similar proteins can be viewed for 3F6U's classification [PROC_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 [PROC_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3F6U
  • Community annotation for 3F6U 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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