1NMD Structural Protein date Jan 09, 2003
title Crystal Structure Of D. Discoideum Actin-Gelsolin Segment 1 Complex Crystallized In Presence Of Lithium Atp
authors S.M.Vorobiev, S.Welti, J.Condeelis, S.C.Almo
compound source
Molecule: Actin
Chain: A
Organism_scientific: Dictyostelium Discoideum
Organism_taxid: 44689

Molecule: Gelsolin
Chain: G
Fragment: Domain I
Synonym: Actin-Depolymerizing Factor, Adf, Brevin, Agel
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gsn
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmw172
symmetry Space Group: C 1 2 1
R_factor 0.203 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
178.912 69.053 56.613 90.00 104.65 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ATP, CA, SO2, SO4 enzyme
related structures by homologous chain: 1T44, 1YAG
Gene
Ontology
ChainFunctionProcessComponent
A


G


Primary referenceThe structure of nonvertebrate actin: implications for the ATP hydrolytic mechanism., Vorobiev S, Strokopytov B, Drubin DG, Frieden C, Ono S, Condeelis J, Rubenstein PA, Almo SC, Proc Natl Acad Sci U S A 2003 May 13;100(10):5760-5. PMID:12732734
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1nmd.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (1nmd.pdb2.gz) 168 Kb
  • LPC: Ligand-Protein Contacts for 1NMD
  • CSU: Contacts of Structural Units for 1NMD
  • Likely Quarternary Molecular Structure file(s) for 1NMD
  • Retrieve 1NMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NMD from S2C, [Save to disk]
  • View 1NMD 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 1NMD
  • 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 1NMD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nmda2, region A:147-375 [Jmol] [rasmolscript] [script source]
        - Domain d1nmda1, region A:4-146 [Jmol] [rasmolscript] [script source]
        - Domain d1nmdg_, region G [Jmol] [rasmolscript] [script source]
  • Fold representative 1nmd 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: [1nmd] [1nmd_G] [1nmd_A]
  • SWISS-PROT database: [P07830] [P06396]
  • Domain organization of [ACT1_DICDI] [GELS_HUMAN] by SWISSPFAM
  • Domains found in 1NMD: [ACTIN] [GEL ] by SMART
  • Alignments of the sequence of 1NMD with the sequences similar proteins can be viewed for 1NMD's classification [ACT1_DICDI] [GELS_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 [ACT1_DICDI] [GELS_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1NMD
  • Community annotation for 1NMD 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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