1QLE

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.309
  • R-Value Work: 0.235

Literature

Macromolecules
Sequence Display for 1QLE

Classification: OXIDOREDUCTASE / IMMUNE SYSTEM

Total Structure Weight: 152419.56

Macromolecule Entities
Molecule Chains Length Organism Details
CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA A 538 Paracoccus denitrificans EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaDII
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE II B 252 Paracoccus denitrificans EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaC coiI ctaB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE III C 273 Paracoccus denitrificans EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaE coiII
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CCYTOCHROME C OXIDASE D 43 Paracoccus denitrificans EC#: 1.9.3.1 IUBMB
Gene Name(s): ctaH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN ANTIBODY FV FRAGMENT H 119 Mus musculus
LIGHT CHAIN ANTIBODY FV FRAGMENT L 108 Mus musculus

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)

Protein Name: Cytochrome C Oxidase, aa3


Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEA
Query on HEA

A HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PC1
Query on PC1

C 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE (Synonym)
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

B DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

A COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.309
  • R-Value Work: 0.235
  • Space Group: P 4

Unit Cell:

Length (Å) Angle (°)
a = 205.20 α = 90.00
b = 205.20 β = 90.00
c = 81.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-08-30
  • Released Date: 1999-12-02
  • Deposition author(s): Harrenga, A., Michel, H.

Revision History

  • Version 1_0: 1999-12-02

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-07-12

    Type: Derived calculations