1GGU Transferase date Jul 22, 1998
title Human Factor Xiii With Calcium Bound In The Ion Site
authors B.A.Fox, V.C.Yee, L.C.Pederson, I.L.Trong, P.D.Bishop, R.E.Stenkamp, D.C.Teller
compound source
Molecule: Protein (Coagulation Factor Xiii)
Chain: A, B
Fragment: Full Length
Ec: 2.3.2.13
Engineered: Yes
Other_details: Calcium Bound In The Ion Site
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932
symmetry Space Group: P 1 21 1
R_factor 0.227 R_Free 0.313
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.172 70.764 133.822 90.00 106.11 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA enzyme Transferase E.C.2.3.2.13 BRENDA
related structures by homologous chain: 1F13, 1FIE
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceIdentification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography., Fox BA, Yee VC, Pedersen LC, Le Trong I, Bishop PD, Stenkamp RE, Teller DC, J Biol Chem 1999 Feb 19;274(8):4917-23. PMID:9988734
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (253 Kb) [Save to disk]
  • Biological Unit Coordinates (1ggu.pdb1.gz) 248 Kb
  • LPC: Ligand-Protein Contacts for 1GGU
  • CSU: Contacts of Structural Units for 1GGU
  • Likely Quarternary Molecular Structure file(s) for 1GGU
  • Retrieve 1GGU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GGU from S2C, [Save to disk]
  • View 1GGU 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 1GGU
  • 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 1GGU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ggua4, region A:191-508 [Jmol] [rasmolscript] [script source]
        - Domain d1ggua2, region A:516-627 [Jmol] [rasmolscript] [script source]
        - Domain d1ggua3, region A:628-727 [Jmol] [rasmolscript] [script source]
        - Domain d1ggua1, region A:8-190 [Jmol] [rasmolscript] [script source]
        - Domain d1ggub4, region B:191-508 [Jmol] [rasmolscript] [script source]
        - Domain d1ggub2, region B:516-627 [Jmol] [rasmolscript] [script source]
        - Domain d1ggub3, region B:628-727 [Jmol] [rasmolscript] [script source]
        - Domain d1ggub1, region B:8-190 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ggu 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: [1ggu] [1ggu_B] [1ggu_A]
  • SWISS-PROT database: [P00488]
  • Domain organization of [F13A_HUMAN] by SWISSPFAM
  • Domain found in 1GGU: [TGc ] by SMART
  • Alignments of the sequence of 1GGU with the sequences similar proteins can be viewed for 1GGU's classification [F13A_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 [F13A_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1GGU
  • Community annotation for 1GGU 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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