1D5S Hydrolase Inhibitor date Oct 11, 1999
title Crystal Structure Of Cleaved Antitrypsin Polymer
authors M.A.Dunstone, W.Dai, J.C.Whisstock, J.Rossjohn, R.N.Pike, S.C.Feil, B.F.Le Bonneic, M.W.Parker, S.P.Bottomley
compound source
Molecule: P1-Arg Antitrypsin
Chain: A
Fragment: N-Terminal Fragment
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: P1-Arg Antitrypsin
Chain: B
Fragment: C-Terminal Fragment
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 42 21 2
R_factor 0.208 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.170 110.170 76.670 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
related structures by homologous chain: 7API, 9API
Primary referenceCleaved antitrypsin polymers at atomic resolution., Dunstone MA, Dai W, Whisstock JC, Rossjohn J, Pike RN, Feil SC, Le Bonniec BF, Parker MW, Bottomley SP, Protein Sci 2000 Feb;9(2):417-20. PMID:10716194
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (1d5s.pdb1.gz) 56 Kb
  • CSU: Contacts of Structural Units for 1D5S
  • Likely Quarternary Molecular Structure file(s) for 1D5S
  • Retrieve 1D5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5S from S2C, [Save to disk]
  • View 1D5S 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 1D5S
  • 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 1D5S, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5s.1, region A:,B [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5s 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: [1d5s_B] [1d5s] [1d5s_A]
  • SWISS-PROT database: [P01009]
  • Domain organization of [A1AT_HUMAN] by SWISSPFAM
  • Domain found in 1D5S: [SERPIN ] by SMART
  • Alignments of the sequence of 1D5S with the sequences similar proteins can be viewed for 1D5S's classification [A1AT_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 [A1AT_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1D5S
  • Community annotation for 1D5S 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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