2QJY

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b
A, D, G, J, M
A, D, G, J, M, P
445Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petBfbcB
Membrane Entity: Yes 
UniProt
Find proteins for Q02761 (Cereibacter sphaeroides)
Explore Q02761 
Go to UniProtKB:  Q02761
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02761
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1
B, E, H, K, N
B, E, H, K, N, Q
269Cereibacter sphaeroidesMutation(s): 0 
Gene Names: fbcC
Membrane Entity: Yes 
UniProt
Find proteins for Q02760 (Cereibacter sphaeroides)
Explore Q02760 
Go to UniProtKB:  Q02760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02760
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit
C, F, I, L, O
C, F, I, L, O, R
187Cereibacter sphaeroidesMutation(s): 1 
Gene Names: petAfbcF
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for Q02762 (Cereibacter sphaeroides)
Explore Q02762 
Go to UniProtKB:  Q02762
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02762
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

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FA [auth D]
JB [auth M]
QA [auth G]
TB [auth P]
W [auth A]
FA [auth D],
JB [auth M],
QA [auth G],
TB [auth P],
W [auth A],
ZA [auth J]
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
HEM
Query on HEM

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AA [auth B]
CA [auth D]
DA [auth D]
DB [auth K]
GB [auth M]
AA [auth B],
CA [auth D],
DA [auth D],
DB [auth K],
GB [auth M],
HB [auth M],
JA [auth E],
NA [auth G],
NB [auth N],
OA [auth G],
QB [auth P],
RB [auth P],
T [auth A],
TA [auth H],
U [auth A],
WA [auth J],
WB [auth Q],
XA [auth J]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SMA
Query on SMA

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EA [auth D]
IB [auth M]
PA [auth G]
SB [auth P]
V [auth A]
EA [auth D],
IB [auth M],
PA [auth G],
SB [auth P],
V [auth A],
YA [auth J]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
UQ2
Query on UQ2

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AB [auth J]
GA [auth D]
KB [auth M]
RA [auth G]
UB [auth P]
AB [auth J],
GA [auth D],
KB [auth M],
RA [auth G],
UB [auth P],
X [auth A]
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
BGL
Query on BGL

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BB [auth K]
HA [auth E]
LA [auth G]
LB [auth N]
PB [auth P]
BB [auth K],
HA [auth E],
LA [auth G],
LB [auth N],
PB [auth P],
Y [auth B]
2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
FES
Query on FES

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BA [auth C]
EB [auth L]
KA [auth F]
OB [auth O]
VA [auth I]
BA [auth C],
EB [auth L],
KA [auth F],
OB [auth O],
VA [auth I],
ZB [auth R]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SR
Query on SR

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CB [auth K]
FB [auth M]
IA [auth E]
MA [auth G]
MB [auth N]
CB [auth K],
FB [auth M],
IA [auth E],
MA [auth G],
MB [auth N],
S [auth A],
SA [auth H],
VB [auth Q],
Z [auth B]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
CL
Query on CL

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UA [auth I],
YB [auth R]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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XB [auth R]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SMA Binding MOAD:  2QJY Kd: 0.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 351.891α = 90
b = 147.042β = 104.25
c = 161.312γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description