1D7K Lyase date Oct 18, 1999
title Crystal Structure Of Human Ornithine Decarboxylase At 2.1 An Resolution
authors J.J.Almrud, M.A.Oliveira, A.D.Kern, N.V.Grishin, M.A.Phillips, M.
compound source
Molecule: Human Ornithine Decarboxylase
Chain: A, B
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Pet With N-Terminal (His)6 Tag
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.288
length a length b length c angle alpha angle beta angle gamma
61.680 107.450 139.710 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand LLP enzyme Lyase E.C. BRENDA
related structures by homologous chain: 1F3T, 1SZR
A, B

Primary referenceCrystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding., Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML, J Mol Biol 2000 Jan 7;295(1):7-16. PMID:10623504
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (1d7k.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 1D7K
  • CSU: Contacts of Structural Units for 1D7K
  • Likely Quarternary Molecular Structure file(s) for 1D7K
  • Retrieve 1D7K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D7K from S2C, [Save to disk]
  • View 1D7K 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 1D7K
  • 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 1D7K, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d7ka2, region A:44-283 [Jmol] [rasmolscript] [script source]
        - Domain d1d7ka1, region A:7-43,A:284-427 [Jmol] [rasmolscript] [script source]
        - Domain d1d7kb2, region B:44-283 [Jmol] [rasmolscript] [script source]
        - Domain d1d7kb1, region B:7-43,B:284-421 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d7k 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: [1d7k_B] [1d7k] [1d7k_A]
  • SWISS-PROT database: [P11926]
  • Domain organization of [DCOR_HUMAN] by SWISSPFAM
  • Other resources with information on 1D7K
  • Community annotation for 1D7K 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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