OCA Atlas for 2WDR

2WDR

Oxidoreductase

date

Mar 25, 2009

title

E. Coli Succinate:Quinone Oxidoreductase (Sqr) With Pentachlorophenol Bound

authors

J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini

compound

source

Molecule: Succinate Dehydrogenase Flavoprotein Subunit
Chain: A, E, I
Ec: 1.3.5.1, 1.3.99.1
Engineered: Yes
Other_details: Fad Atom C8m Is Covalently Linked To Ne2 Of His45;

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dw35
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pfas

Molecule: Succinate Dehydrogenase Iron-Sulfur Subunit
Chain: B, F, J
Ec: 1.3.5.1, 1.3.99.1
Engineered: Yes

Molecule: Succinate Dehydrogenase Cytochrome B556 Subunit
Chain: C, G, K
Ec: 1.3.5.1
Engineered: Yes
Other_details: Residues 8-129 Modelled

Molecule: Succinate Dehydrogenase Hydrophobic Membrane Anch Subunit;
Chain: D, H, L
Ec: 1.3.5.1
Engineered: Yes
Other_details: Residues 11-115 Modelled

symmetry

Space Group: P 21 21 21

R_factor

0.197

R_Free

0.228

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
119.955	186.128	204.034	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.20 Å

ligand

F3S, FAD, FES, HEM, NA, PCI, SF4, TEO

enzyme

Oxidoreductase E.C.1.3.5.1 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, E, I
F, J, B
H, D, L	electron transfer activity
K, C, G	electron transfer activity

Primary reference

Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site., Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G, J Biol Chem. 2009 Aug 25. PMID:19710024

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (496 Kb) [Save to disk]

Biological Unit Coordinates (2wdr.pdb1.gz) 166 Kb

Biological Unit Coordinates (2wdr.pdb2.gz) 166 Kb

Biological Unit Coordinates (2wdr.pdb3.gz) 167 Kb

LPC: Ligand-Protein Contacts for 2WDR

CSU: Contacts of Structural Units for 2WDR

Structure Factors (2045 Kb)

Retrieve 2WDR in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2WDR from S2C, [Save to disk]

Re-refined 2wdr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2WDR 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 2WDR

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 2WDR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2wdr_J] [2wdr_I] [2wdr_G] [2wdr_K] [2wdr_L] [2wdr_E] [2wdr] [2wdr_H] [2wdr_F] [2wdr_A] [2wdr_D] [2wdr_C] [2wdr_B]

SWISS-PROT database: [P0AC41] [P07014] [P69054] [P0AC44]

Domain organization of [DHSA_ECOLI] [DHSB_ECOLI] [DHSC_ECOLI] [DHSD_ECOLI] by SWISSPFAM

Other resources with information on 2WDR

Community annotation for 2WDR 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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