1BNL Extracellular Matrix date Jul 30, 1998
title Zinc Dependent Dimers Observed In Crystals Of Human Endostatin
authors Y.H.Ding, K.Javaherian, K.M.Lo, R.Chopra, T.Boehm, J.Lanciotti, B.A.Harris, Y.Li, R.Shapiro, E.Hohenester, R.Timpl, J.Folkman, D.C.Wiley
compound source
Molecule: Collagen Xviii
Chain: A, B, C, D
Fragment: Endostatin, 20-Kda Collagen Xviii C-Terminal Globular Domain;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Secreted
Gene: Collagen Xviii
Expression_system: Ns0 Murine Myeloma Cells
Expression_system_plasmid: Pdcs-Fc(D4k)
symmetry Space Group: C 1 2 1
R_factor 0.240 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.713 74.266 137.805 90.00 102.55 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand ZN enzyme
related structures by homologous chain: 1DY0
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceZinc-dependent dimers observed in crystals of human endostatin., Ding YH, Javaherian K, Lo KM, Chopra R, Boehm T, Lanciotti J, Harris BA, Li Y, Shapiro R, Hohenester E, Timpl R, Folkman J, Wiley DC, Proc Natl Acad Sci U S A 1998 Sep 1;95(18):10443-8. PMID:9724722
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (1bnl.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (1bnl.pdb2.gz) 29 Kb
  • Biological Unit Coordinates (1bnl.pdb3.gz) 29 Kb
  • Biological Unit Coordinates (1bnl.pdb4.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 1BNL
  • CSU: Contacts of Structural Units for 1BNL
  • Likely Quarternary Molecular Structure file(s) for 1BNL
  • Retrieve 1BNL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BNL from S2C, [Save to disk]
  • View 1BNL 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 1BNL
  • 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 1BNL, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bnla_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1bnlb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1bnlc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1bnld_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1bnl 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: [1bnl_C] [1bnl] [1bnl_A] [1bnl_D] [1bnl_B]
  • SWISS-PROT database: [P39060]
  • Domain organization of [COIA1_HUMAN] by SWISSPFAM
  • Other resources with information on 1BNL
  • Community annotation for 1BNL 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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