spacer
spacer

PDBsum entry 3cwb

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3cwb
Jmol
Contents
Protein chains
443 a.a. *
421 a.a. *
380 a.a. *
241 a.a. *
196 a.a. *
100 a.a. *
81 a.a. *
70 a.a. *
51 a.a. *
61 a.a. *
Ligands
HEM ×4
PEE ×6
ICX ×2
_UQ ×2
AZI ×2
BOG ×6
HEC ×2
CDL ×4
FES ×2
UNL ×4
Waters ×16
* Residue conservation analysis
PDB id:
3cwb
Name: Oxidoreductase
Title: Chicken cytochrome bc1 complex inhibited by an iodinated ana the polyketide crocacin-d
Structure: Mitochondrial ubiquinol-cytochromE-C reductase co protein i. Chain: a, n. Mitochondrial ubiquinol-cytochromE-C reductase co protein 2. Chain: b, o. Cytochrome b. Chain: c, p. Synonym: ubiquinol-cytochromE-C reductase complex cytochrom
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organism_taxid: 9031
Resolution:
3.51Å     R-factor:   0.285     R-free:   0.319
Authors: L.Huang,T.Cromartie,R.Viner,P.J.Crowley,E.A.Berry
Key ref: P.J.Crowley et al. (2008). The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Bioorg Med Chem, 16, 10345-10355. PubMed id: 18996700
Date:
21-Apr-08     Release date:   12-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 443 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX29  (D0VX29_CHICK) -  Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2
Seq:
Struc:
441 a.a.
421 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX31  (D0VX31_CHICK) -  Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i
Seq:
Struc:
446 a.a.
421 a.a.*
Protein chains
Pfam   ArchSchema ?
P18946  (CYB_CHICK) -  Cytochrome b
Seq:
Struc:
380 a.a.
380 a.a.
Protein chains
No UniProt id for this chain
Struc: 241 a.a.
Protein chains
Pfam   ArchSchema ?
Q5ZLR5  (UCRI_CHICK) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
272 a.a.
196 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX30  (D0VX30_CHICK) -  Cytochrome b-c1 complex subunit 7
Seq:
Struc:
110 a.a.
100 a.a.*
Protein chains
Pfam   ArchSchema ?
D0VX32  (D0VX32_CHICK) -  Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
Seq:
Struc:
81 a.a.
81 a.a.
Protein chains
Pfam   ArchSchema ?
D0VX28  (D0VX28_CHICK) -  Cytochrome b-c1 complex subunit 6
Seq:
Struc:
77 a.a.
70 a.a.
Protein chains
Pfam   ArchSchema ?
Q5ZLR5  (UCRI_CHICK) -  Cytochrome b-c1 complex subunit Rieske, mitochondrial
Seq:
Struc:
272 a.a.
51 a.a.*
Protein chains
No UniProt id for this chain
Struc: 61 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 338 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains B, E, G, I, N, P, R, V, W: E.C.1.10.2.2  - Quinol--cytochrome-c reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Quinol + 2 ferricytochrome c = quinone + 2 ferrocytochrome c + 2 H+
Quinol
Bound ligand (Het Group name = UQ)
matches with 82.61% similarity
+
2 × ferricytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity
= quinone
+ 2 × ferrocytochrome c
+ 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   8 terms 
  Biological process     mitochondrial electron transport, ubiquinol to cytochrome c   5 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
Bioorg Med Chem 16:10345-10355 (2008)
PubMed id: 18996700  
 
 
The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.
P.J.Crowley, E.A.Berry, T.Cromartie, F.Daldal, C.R.Godfrey, D.W.Lee, J.E.Phillips, A.Taylor, R.Viner.
 
  ABSTRACT  
 
Extensive molecular modeling based on crystallographic data was used to aid the design of synthetic analogues of the fungicidal naturally occurring respiration inhibitors crocacins A and D, and an inhibitor binding model to the mammalian cytochrome bc(1) complex was constructed. Simplified analogues were made which showed high activity in a mitochondrial beef heart respiration assay, and which were also active against certain plant pathogens in glasshouse tests. A crystal structure was obtained of an analogue of crocacin D bound to the chicken heart cytochrome bc(1) complex, which validated the binding model and which confirmed that the crocacins are a new class of inhibitor of the cytochrome bc(1) complex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21286632 C.F.Nising, S.Hillebrand, and L.Rodefeld (2011).
Recent developments in the total synthesis of fungicidal natural products--a crop protection perspective.
  Chem Commun (Camb), 47, 4062-4073.  
20520915 K.J.Weissman, and R.Müller (2010).
Myxobacterial secondary metabolites: bioactivities and modes-of-action.
  Nat Prod Rep, 27, 1276-1295.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.