2YEV

Structure of caa3-type cytochrome oxidase

Structural Biology Knowledgebase: 2YEV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YEV

Classification: ELECTRON TRANSPORT

Total Structure Weight: 277443.44

Macromolecule Entities
Molecule Chains Length Organism Details
CYTOCHROME C OXIDASE POLYPEPTIDE I+III A, D 791 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Details: COVALENT LINK BETWEEN HIS 250 NE2 AND TYR 254 CE2
Gene Name(s): caaA ctaD TTHA0312
CYTOCHROME C OXIDASE SUBUNIT 2 B, E 337 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Details: COVALENT LINK BETWEEN CYS SG 247 AND HEC CAB 587 COVALENT LINK BETWEEN CYS SG 250 AND HEC CAC 587
Gene Name(s): TTHA0311
CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV C, F 66 Thermus thermophilus EC#: 1.9.3.1 IUBMB
Details: N-FORMYL GROUP ON MET 1
Gene Name(s): TTHA1863

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

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

Protein Name: Cytochrome C Oxidase, caa3


Small Molecules
Ligands 10 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
5PL
Query on 5PL

A, D (1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA- D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1- {[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO- 7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1- YL 15-METHYLHEXADECANOATE
C67 H129 N2 O15 P
LEQHPGOQHCQGAI-TYASGWLASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HAS
Query on HAS

A, D HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-QIHJKJTBDH
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEC
Query on HEC

B, E HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
4AG
Query on 4AG

A (2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE
SN-1,2-DIPALMITOYL DIACYLGLYCEROL (Synonym)
C35 H68 O5
JEJLGIQLPYYGEE-MGBGTMOVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
7E8
Query on 7E8

A (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7- ENOATE
7.7 MAG (Synonym)
C17 H32 O4
LVBAGTJIDOCNIJ-XITLMJRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
7E9
Query on 7E9

B 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE
C17 H32 O4
SSMGVWSPWWDBRB-FPLPWBNLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

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

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

C, D, F CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FME
Query on FME
C, F L-PEPTIDE LINKING C6 H11 N O3 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.171
  • Space Group: I 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.25 α = 90.00
b = 76.03 β = 92.21
c = 300.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-31
  • Released Date: 2012-05-23
  • Deposition author(s): Lyons, J.A., Aragao, D., Soulimane, T., Caffrey, M.

Revision History

  • 2015-04-29
    Type: Data collection | Details: REMARK 200
  • 2012-08-01
    Type: Citation | Details: JRNL
  • 2012-06-27
    Type: Other | Details: Citation