6MYP

Avian mitochondrial complex II with TTFA (thenoyltrifluoroacetone) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.235 

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-binding 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 13 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
SF4
Query on SF4

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Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 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
TTF
Query on TTF

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Download CCD File 
C
4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE
2-THENOYLTRIFLUOROACETONE
C8 H5 F3 O2 S
TXBBUSUXYMIVOS-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 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
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 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

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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: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.951α = 90.00
b = 84.303β = 90.00
c = 290.194γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

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