OCA Atlas for 1WDK

1WDK

Lyase,Oxidoreductase Transferase

date

May 17, 2004

title

Fatty Acid Beta-Oxidation Multienzyme Complex From Pseudomon Form I (Native2)

authors

M.Ishikawa, D.Tsuchiya, T.Oyama, Y.Tsunaka, K.Morikawa

compound

source

Molecule: Fatty Oxidation Complex Alpha Subunit
Chain: A, B
Synonym: Fatty Acid Beta-Oxidation Multienzyme Complex, Alp Subunit;
Ec: 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3
Engineered: Yes

Organism_scientific: Pseudomonas Fragi
Organism_taxid: 296
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Mif100
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt7-7

Molecule: 3-Ketoacyl-Coa Thiolase
Chain: C, D
Synonym: Fatty Acid Beta-Oxidation Multienzyme Complex, Bet Fatty Oxidation Complex Beta Subunit; Beta-Ketothiolase; Ac Acyltransferase;
Ec: 2.3.1.16
Engineered: Yes

symmetry

Space Group: C 1 2 1

R_factor

0.203

R_Free

0.244

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
180.705	94.578	160.001	90.00	111.45	90.00

method

X-Ray Diffraction

resolution

2.50 Å

ligand

ACO, HG, N8E, NAD, ZN

enzyme

Lyase E.C.4.2.1.17 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, B
D, C

Primary reference

Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex., Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K, EMBO J 2004 Jul 21;23(14):2745-54. Epub 2004 Jul 1. PMID:15229654

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (358 Kb) [Save to disk]

Biological Unit Coordinates (1wdk.pdb1.gz) 350 Kb

LPC: Ligand-Protein Contacts for 1WDK

CSU: Contacts of Structural Units for 1WDK

Likely Quarternary Molecular Structure file(s) for 1WDK

Structure Factors (724 Kb)

Retrieve 1WDK in mmCIF format [Save to disk]

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

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

View 1WDK 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 1WDK

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 1WDK, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1wdka4, region A:1-310 [Jmol] [rasmolscript] [script source]
- Domain d1wdka3, region A:311-496 [Jmol] [rasmolscript] [script source]
- Domain d1wdka1, region A:496-620 [Jmol] [rasmolscript] [script source]
- Domain d1wdka2, region A:621-715 [Jmol] [rasmolscript] [script source]
- Domain d1wdkb4, region B:1-310 [Jmol] [rasmolscript] [script source]
- Domain d1wdkb3, region B:311-496 [Jmol] [rasmolscript] [script source]
- Domain d1wdkb1, region B:496-620 [Jmol] [rasmolscript] [script source]
- Domain d1wdkb2, region B:621-715 [Jmol] [rasmolscript] [script source]
- Domain d1wdkc1, region C:2-263 [Jmol] [rasmolscript] [script source]
- Domain d1wdkc2, region C:264-391 [Jmol] [rasmolscript] [script source]
- Domain d1wdkd1, region D:2-263 [Jmol] [rasmolscript] [script source]
- Domain d1wdkd2, region D:264-391 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1wdk] [1wdk_D] [1wdk_B] [1wdk_C] [1wdk_A]

SWISS-PROT database: [P28790] [P28793]

Domain organization of [FADA_PSEFR] [FADB_PSEFR] by SWISSPFAM

Other resources with information on 1WDK

Community annotation for 1WDK at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]