OCA Atlas for 1UJ3

1UJ3

Immune System Blood Clotting

date

Jul 25, 2003

title

Crystal Structure Of A Humanized Fab Fragment Of Anti-Tissue Antibody In Complex With Tissue Factor

authors

U.Ohto, R.Mizutani, M.Nakamura, H.Adachi, Y.Satow

compound

source

Molecule: Igg Fab Light Chain
Chain: A
Fragment: Anti-Tissue-Factor Antibody Hatr-5 Fab
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Igg Fab Heavy Chain
Chain: B
Fragment: Anti-Tissue-Factor Antibody Hatr-5 Fab
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tissue Factor
Chain: C
Fragment: Residues 606-810
Synonym: Tf, Coagulation Factor III, Thromboplastin, Cd142 Blood Coagulation Factor;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

symmetry

Space Group: P 21 21 2

R_factor

0.196

R_Free

0.227

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
103.054	265.996	42.254	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.10 Å

related structures

by homologous chain: 1C5B, 1FAK, 1O5D, 1TJH

Gene
Ontology

Chain	Function	Process	Component
C

Primary reference

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor., Ohto U, Mizutani R, Nakamura M, Adachi H, Satow Y, J Synchrotron Radiat 2004 Jan 1;11(Pt 1):105-8. PMID:14646147

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]

Biological Unit Coordinates (1uj3.pdb1.gz) 108 Kb

CSU: Contacts of Structural Units for 1UJ3

Likely Quarternary Molecular Structure file(s) for 1UJ3

Structure Factors (512 Kb)

Retrieve 1UJ3 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1UJ3 from S2C, [Save to disk]

Re-refined 1uj3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1UJ3 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 1UJ3

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 1UJ3, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1uj3a1, region A:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1uj3a2, region A:108-214 [Jmol] [rasmolscript] [script source]
- Domain d1uj3b1, region B:301-417 [Jmol] [rasmolscript] [script source]
- Domain d1uj3b2, region B:418-517 [Jmol] [rasmolscript] [script source]
- Domain d1uj3c1, region C:606-706 [Jmol] [rasmolscript] [script source]
- Domain d1uj3c2, region C:707-810 [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: [1uj3_A] [1uj3_C] [1uj3_B] [1uj3]

SWISS-PROT database: [P13726]

Domain organization of [TF_HUMAN] by SWISSPFAM

Domains found in 1UJ3: [IG_like] [IGv ] by SMART

Other resources with information on 1UJ3

Community annotation for 1UJ3 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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