6MYO

Avian mitochondrial complex II with flutolanyl bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystallographic studies of the binding of ligands to the Ubiquinone site of Mitochondrial Respiratory Complex II

Huang, L.-S.Berry, E.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
A
621Gallus gallusMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Find proteins for F1NPJ4 (Gallus gallus)
Go to Gene View: SDHA
Go to UniProtKB:  F1NPJ4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
B
252Gallus gallusMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Find proteins for Q9YHT2 (Gallus gallus)
Go to Gene View: SDHB
Go to UniProtKB:  Q9YHT2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome b, large subunit
C
140Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Find proteins for D0VWW3 (Gallus gallus)
Go to UniProtKB:  D0VWW3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D
103Gallus gallusMutation(s): 0 
Gene Names: SDHD
Find proteins for Q5ZIS0 (Gallus gallus)
Go to Gene View: SDHD
Go to UniProtKB:  Q5ZIS0
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FTN
Query on FTN

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C
N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl)benzamide
flutolanil, N-(3-Isopropoxy-phenyl)-2-trifluoromethylbenzamide
C17 H16 F3 N O2
PTCGDEVVHUXTMP-UHFFFAOYSA-N
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

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B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA

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A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
UMQ
Query on UMQ

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C
UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
3PE
Query on 3PE

Download SDF File 
Download CCD File 
D
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
C
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.637α = 90.00
b = 83.783β = 90.00
c = 289.575γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PHENIXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human ServicesUnited States1R01GM062563

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release