1LWU Blood Clotting date Jun 03, 2002
title Crystal Structure Of Fragment D From Lamprey Fibrinogen Comp The Peptide Gly-His-Arg-Pro-Amide
authors Z.Yang, G.Spraggon, L.Pandi, S.J.Everse, M.Riley, R.F.Doolittle
compound source
Molecule: Fibrinogen Alpha-1 Chain
Chain: A, D, G, J
Fragment: Fragment
Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757

Molecule: Fibrinogen Beta Chain
Chain: B, E, H, K
Fragment: Segment 2 Of 2

Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757

Molecule: Fibrinogen Gamma Chain
Chain: C, F, I, L

Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757

Molecule: Ligand Gly-His-Arg-Pro-Nh2
Chain: M, N, O, P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1
R_factor 0.245 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.735 47.654 244.650 88.81 97.23 86.17
method X-Ray Diffractionresolution 2.80 Å
ligand BMA, CA, GAL, MAN, NAG, NDG, NH2 enzyme
related structures by homologous chain: 1FIC, 1N73
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


F, C, I, L


K, E, B, H


Primary referenceCrystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide., Yang Z, Spraggon G, Pandi L, Everse SJ, Riley M, Doolittle RF, Biochemistry 2002 Aug 13;41(32):10218-24. PMID:12162736
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (498 Kb) [Save to disk]
  • Biological Unit Coordinates (1lwu.pdb1.gz) 247 Kb
  • Biological Unit Coordinates (1lwu.pdb2.gz) 248 Kb
  • LPC: Ligand-Protein Contacts for 1LWU
  • CSU: Contacts of Structural Units for 1LWU
  • Likely Quarternary Molecular Structure file(s) for 1LWU
  • Retrieve 1LWU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LWU from S2C, [Save to disk]
  • View 1LWU 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 1LWU
  • 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 1LWU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lwua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1lwub2, region B:163-218 [Jmol] [rasmolscript] [script source]
        - Domain d1lwub1, region B:219-477 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuc1, region C:138-399 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuc2, region C:83-137 [Jmol] [rasmolscript] [script source]
        - Domain d1lwud_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1lwue2, region E:163-218 [Jmol] [rasmolscript] [script source]
        - Domain d1lwue1, region E:219-477 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuf1, region F:138-399 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuf2, region F:83-137 [Jmol] [rasmolscript] [script source]
        - Domain d1lwug_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1lwuh2, region H:163-218 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuh1, region H:219-477 [Jmol] [rasmolscript] [script source]
        - Domain d1lwui1, region I:138-395 [Jmol] [rasmolscript] [script source]
        - Domain d1lwui2, region I:83-137 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1lwuk2, region K:163-218 [Jmol] [rasmolscript] [script source]
        - Domain d1lwuk1, region K:219-477 [Jmol] [rasmolscript] [script source]
        - Domain d1lwul1, region L:138-395 [Jmol] [rasmolscript] [script source]
        - Domain d1lwul2, region L:83-137 [Jmol] [rasmolscript] [script source]
  • Fold representative 1lwu 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: [1lwu_L] [1lwu_G] [1lwu_M] [1lwu_O] [1lwu] [1lwu_K] [1lwu_P] [1lwu_J] [1lwu_D] [1lwu_N] [1lwu_I] [1lwu_E] [1lwu_F] [1lwu_C] [1lwu_B] [1lwu_A] [1lwu_H]
  • SWISS-PROT database: [P02674] [P02678] [P04115]
  • Domain organization of [FIBA1_PETMA] [FIBB_PETMA] [FIBG_PETMA] by SWISSPFAM
  • Domain found in 1LWU: [FBG ] by SMART
  • Other resources with information on 1LWU
  • Community annotation for 1LWU 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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