OCA Atlas for 1LTJ

1LTJ

Blood Clotting

date

May 20, 2002

title

Crystal Structure Of Recombinant Human Fibrinogen Fragment D Peptide Ligands Gly-Pro-Arg-Pro-Amide And Gly-His-Arg-Pro-A

authors

M.S.Kostelansky, L.Betts, O.V.Gorkun, S.T.Lord

compound

source

Molecule: Fibrinogen Alphaalpha-E Chain
Chain: A, D
Fragment: Fragment D (Residues 126-191)
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells

Molecule: Fibrinogen Beta Chain
Chain: B, E
Fragment: Fragment D (Residues 149-461)
Engineered: Yes

Molecule: Fibrinogen Gamma Chain
Chain: C, F
Fragment: Fragment D (Residues 96-406)
Engineered: Yes

Molecule: Gly-Pro-Arg-Pro
Chain: G, I
Engineered: Yes

Synthetic: Yes

Molecule: Gly-His-Arg-Pro
Chain: H, J
Engineered: Yes

Synthetic: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.212

R_Free

0.270

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
89.284	94.218	226.936	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.80 Å

ligand

CA, FUC, NAG

enzyme

related structures

by homologous chain: 1FZF, 1LT9

Gene
Ontology

Chain	Function	Process	Component
A, D
E, B
F, C

Primary reference

2.8 A crystal structures of recombinant fibrinogen fragment D with and without two peptide ligands: GHRP binding to the "b" site disrupts its nearby calcium-binding site., Kostelansky MS, Betts L, Gorkun OV, Lord ST, Biochemistry 2002 Oct 8;41(40):12124-32. PMID:12356313

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk]

Biological Unit Coordinates (1ltj.pdb1.gz) 111 Kb

Biological Unit Coordinates (1ltj.pdb2.gz) 109 Kb

LPC: Ligand-Protein Contacts for 1LTJ

CSU: Contacts of Structural Units for 1LTJ

Likely Quarternary Molecular Structure file(s) for 1LTJ

Structure Factors (526 Kb)

Retrieve 1LTJ in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1LTJ from S2C, [Save to disk]

Re-refined 1ltj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1LTJ 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 1LTJ

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1LTJ, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1ltja_, region A [Jmol] [rasmolscript] [script source]
- Domain d1ltjb2, region B:161-199 [Jmol] [rasmolscript] [script source]
- Domain d1ltjb1, region B:200-458 [Jmol] [rasmolscript] [script source]
- Domain d1ltjc1, region C:142-394 [Jmol] [rasmolscript] [script source]
- Domain d1ltjc2, region C:96-141 [Jmol] [rasmolscript] [script source]
- Domain d1ltjd_, region D [Jmol] [rasmolscript] [script source]
- Domain d1ltje2, region E:165-199 [Jmol] [rasmolscript] [script source]
- Domain d1ltje1, region E:200-458 [Jmol] [rasmolscript] [script source]
- Domain d1ltjf2, region F:110-141 [Jmol] [rasmolscript] [script source]
- Domain d1ltjf1, region F:142-394 [Jmol] [rasmolscript] [script source]

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: [1ltj_B] [1ltj_H] [1ltj_I] [1ltj_A] [1ltj] [1ltj_D] [1ltj_J] [1ltj_C] [1ltj_G] [1ltj_F] [1ltj_E]

SWISS-PROT database: [P02671] [P02675] [P02679]

Domain organization of [FIBA_HUMAN] [FIBB_HUMAN] [FIBG_HUMAN] by SWISSPFAM

Domain found in 1LTJ: [FBG ] by SMART

Other resources with information on 1LTJ

Community annotation for 1LTJ 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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