OCA Atlas for 2BCC

2BCC

Oxidoreductase

date

Sep 18, 1998

title

Stigmatellin-Bound Cytochrome Bc1 Complex From Chicken

authors

Z.Zhang, L.Huang, V.M.Shulmeister, Y.I.Chi, K.K.Kim, L.W.Hung, A.R E.A.Berry, S.H.Kim

compound

source

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: A
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Organ: Heart
Tissue: Muscle
Organelle: Mitochondria
Cellular_location: Mitochondrial Inner Membrane
Other_details: Isolated From Tissue

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: B
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: C
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: D
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: E
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: F
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: G
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: H
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: I
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

Molecule: Ubiquinol Cytochrome C Oxidoreductase
Chain: J
Synonym: Cytochrome Bc1 Complex, Complex III
Ec: 1.10.2.2
Other_details: Model Include Qo-Site Inhibitor Stigmatellin

symmetry

Space Group: P 21 21 21

R_factor

0.284

R_Free

0.317

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
173.460	182.450	241.330	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.50 Å

ligand

BOG, FES, HEM, PEE, SIG, U10

enzyme

Oxidoreductase E.C.1.10.2.2 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A
B
C
D
E
F
G
H
J

Primary reference

Electron transfer by domain movement in cytochrome bc1., Zhang Z, Huang L, Shulmeister VM, Chi YI, Kim KK, Hung LW, Crofts AR, Berry EA, Kim SH, Nature. 1998 Apr 16;392(6677):677-84. PMID:9565029

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (324 Kb) [Save to disk]

Biological Unit Coordinates (2bcc.pdb1.gz) 314 Kb

LPC: Ligand-Protein Contacts for 2BCC

CSU: Contacts of Structural Units for 2BCC

Likely Quarternary Molecular Structure file(s) for 2BCC

Structure Factors (1233 Kb)

Retrieve 2BCC in mmCIF format [Save to disk]

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

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

View 2BCC 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 2BCC

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 2BCC, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d2bcca2, region A:233-445 [Jmol] [rasmolscript] [script source]
- Domain d2bcca1, region A:4-232 [Jmol] [rasmolscript] [script source]
- Domain d2bccb1, region B:18-235 [Jmol] [rasmolscript] [script source]
- Domain d2bccb2, region B:236-439 [Jmol] [rasmolscript] [script source]
- Domain d2bccc3, region C:2-261 [Jmol] [rasmolscript] [script source]
- Domain d2bccc2, region C:262-380 [Jmol] [rasmolscript] [script source]
- Domain d2bccd2, region D:1-195 [Jmol] [rasmolscript] [script source]
- Domain d2bccd3, region D:196-241 [Jmol] [rasmolscript] [script source]
- Domain d2bcce2, region E:1-69 [Jmol] [rasmolscript] [script source]
- Domain d2bcce1, region E:70-196 [Jmol] [rasmolscript] [script source]
- Domain d2bccf_, region F [Jmol] [rasmolscript] [script source]
- Domain d2bccg_, region G [Jmol] [rasmolscript] [script source]
- Domain d2bcch_, region H [Jmol] [rasmolscript] [script source]
- Domain d2bccj_, region J [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: [2bcc_F] [2bcc_J] [2bcc_H] [2bcc_E] [2bcc_G] [2bcc] [2bcc_B] [2bcc_A] [2bcc_D] [2bcc_I] [2bcc_C]

SWISS-PROT database: [P00125] [P18946] [P31800] [P00126] [P00129] [P13271] [P00130] [P13272]

Belongs to the proton-translocating quinol:cytochrome c reductase (qcr) superfamily

according to TCDB.

Domain organization of [CY1_BOVIN] [CYB_CHICK] [QCR1_BOVIN] [QCR6_BOVIN] [QCR7_BOVIN] [QCR8_BOVIN] [QCR9_BOVIN] [UCRI_BOVIN] by SWISSPFAM

Other resources with information on 2BCC

Community annotation for 2BCC 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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