1DM4 Hydrolase date Dec 13, 1999
title Ser195ala Mutant Of Human Thrombin Complexed With Fibrinopep 16)
authors R.Krishnan, E.J.Sadler, A.Tulinsky
compound source
Molecule: Protein (Alpha Thrombin:Light Chain)
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein (Mutant Alpha Thrombin:Heavy Chain)
Chain: B
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein (Fibrinopeptide)
Chain: C
Fragment: Fpa
Engineered: Yes
Other_details: Chemically Synthesized

Synthetic: Yes
symmetry Space Group: I 21 3
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.100 135.100 135.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ACE enzyme
related structures by homologous chain: 1ETT, 4THN
Primary referenceStructure of the Ser195Ala mutant of human alpha--thrombin complexed with fibrinopeptide A(7--16): evidence for residual catalytic activity., Krishnan R, Sadler JE, Tulinsky A, Acta Crystallogr D Biol Crystallogr 2000 Apr;56 ( Pt 4):406-10. PMID:10739913
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1dm4.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (1dm4.pdb2.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 1DM4
  • CSU: Contacts of Structural Units for 1DM4
  • Likely Quarternary Molecular Structure file(s) for 1DM4
  • Retrieve 1DM4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DM4 from S2C, [Save to disk]
  • View 1DM4 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 1DM4
  • 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 1DM4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dm4.1, region A:,B [Jmol] [rasmolscript] [script source]
  • Fold representative 1dm4 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: [1dm4_C] [1dm4] [1dm4_A] [1dm4_B]
  • SWISS-PROT database: [P00734]
  • Domain organization of [THRB_HUMAN] by SWISSPFAM
  • Domain found in 1DM4: [Tryp_SPc ] by SMART
  • Alignments of the sequence of 1DM4 with the sequences similar proteins can be viewed for 1DM4's classification [THRB_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 [THRB_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DM4
  • Community annotation for 1DM4 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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