1D5L Oxidoreductase date Oct 07, 1999
title Crystal Structure Of Cyanide-Bound Human Myeloperoxidase Iso Ph 5.5
authors T.J.Fiedler, C.A.Davey, R.E.Fenna
compound source
Molecule: Myeloperoxidase
Chain: A, B
Fragment: Light Chain
Ec: 1.11.1.7
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood
Cell: Neutrophil

Molecule: Myeloperoxidase
Chain: C, D
Fragment: Heavy Chain
Ec: 1.11.1.7

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood
Cell: Neutrophil
symmetry Space Group: P 1 21 1
R_factor 0.172 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.215 63.507 92.337 90.00 97.43 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACT, BMA, CA, CL, CSO, CYN, FUC, HEM, MAN, NAG, SO4 enzyme Oxidoreductase E.C.1.11.1.7 BRENDA
related structures by homologous chain: 1DNU, 1DNW
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceHuman myeloperoxidase: structure of a cyanide complex and its interaction with bromide and thiocyanate substrates at 1.9 A resolution., Blair-Johnson M, Fiedler T, Fenna R, Biochemistry 2001 Nov 20;40(46):13990-7. PMID:11705390
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (210 Kb) [Save to disk]
  • Biological Unit Coordinates (1d5l.pdb1.gz) 203 Kb
  • Biological Unit Coordinates (1d5l.pdb2.gz) 104 Kb
  • Biological Unit Coordinates (1d5l.pdb3.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 1D5L
  • CSU: Contacts of Structural Units for 1D5L
  • Likely Quarternary Molecular Structure file(s) for 1D5L
  • Structure Factors (619 Kb)
  • Retrieve 1D5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5L from S2C, [Save to disk]
  • Re-refined 1d5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D5L 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 1D5L
  • 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 1D5L, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5l.1, region A:,C [Jmol] [rasmolscript] [script source]
        - Domain d1d5l.2, region B:,D [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5l 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: [1d5l_A] [1d5l_D] [1d5l] [1d5l_C] [1d5l_B]
  • SWISS-PROT database: [P05164]
  • Domain organization of [PERM_HUMAN] by SWISSPFAM
  • Other resources with information on 1D5L
  • Community annotation for 1D5L 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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