OCA Atlas for 2WP9

2WP9

Oxidoreductase

date

Aug 03, 2009

title

Crystal Structure Of The E. Coli Succinate:Quinone Oxidoredu (Sqr) Sdhb His207thr Mutant

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
Mutation: Yes

Molecule: Succinate Dehydrogenase Cytochrome B556 Subunit
Chain: C, G, K
Synonym: Succinate Dehydrogenase Cytochrome B-556 Subunit, B-556;
Ec: 1.3.5.1
Engineered: Yes
Other_details: Residues 8-129 Modelled

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

symmetry

Space Group: P 21 21 21

R_factor

0.190

R_Free

0.222

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
119.853	183.803	202.777	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.70 Å

ligand

CBE, F3S, FAD, FES, HEM, NA, 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

Perturbation of the quinone binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster., Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, Cecchini G, J Biol Chem. 2011 Feb 10. PMID:21310949

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1031 Kb) [Save to disk]

Biological Unit Coordinates (2wp9.pdb1.gz) 340 Kb

Biological Unit Coordinates (2wp9.pdb2.gz) 347 Kb

Biological Unit Coordinates (2wp9.pdb3.gz) 349 Kb

LPC: Ligand-Protein Contacts for 2WP9

CSU: Contacts of Structural Units for 2WP9

Structure Factors (3336 Kb)

Retrieve 2WP9 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 2WP9 from S2C, [Save to disk]

Re-refined 2wp9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2WP9 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 2WP9

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 2WP9, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2wp9_E] [2wp9_F] [2wp9_J] [2wp9_G] [2wp9_K] [2wp9_B] [2wp9_L] [2wp9_A] [2wp9_H] [2wp9_I] [2wp9_D] [2wp9] [2wp9_C]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 2WP9

Community annotation for 2WP9 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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