PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2WU5
Biol. Unit 1
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (362 KB)
Biol.Unit 2 (358 KB)
Biol.Unit 3 (365 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE E. COLI SUCCINATE:QUINONE OXIDOREDUCTASE (SQR) SDHD HIS71MET MUTANT
Authors
:
J. Ruprecht, V. Yankovskaya, E. Maklashina, S. Iwata, G. Cecchini
Date
:
29 Sep 09 (Deposition) - 25 Aug 10 (Release) - 25 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: E,F,G,H (1x)
Biol. Unit 2: A,B,C,D (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Cell Inner Membrane, Tricarboxylic Acid Cycle, Metal-Binding, Transmembrane, Transport, Flavoprotein, Oxidoreductase, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Ruprecht, V. Yankovskaya, E. Maklashina, S. Iwata, G. Cecchini
Crystal Structure Of The E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd His71Met Mutant
To Be Published
[
close entry info
]
Hetero Components
(7, 7)
Info
All Hetero Components
1a: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-... (CBEa)
1b: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-... (CBEb)
1c: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-... (CBEc)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
4c: FE2/S2 (INORGANIC) CLUSTER (FESc)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
5b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
5c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
8a: MALATE LIKE INTERMEDIATE (TEOa)
8b: MALATE LIKE INTERMEDIATE (TEOb)
8c: MALATE LIKE INTERMEDIATE (TEOc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CBE
1
Ligand/Ion
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMI
2
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
3
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
NA
-1
Ligand/Ion
SODIUM ION
7
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
8
TEO
1
Ligand/Ion
MALATE LIKE INTERMEDIATE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC6 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC8 (SOFTWARE)
7: CC1 (SOFTWARE)
8: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
GLY E:14 , ALA E:15 , GLY E:16 , GLY E:17 , ALA E:18 , SER E:37 , LYS E:38 , VAL E:39 , SER E:44 , HIS E:45 , THR E:46 , SER E:48 , ALA E:49 , GLN E:50 , GLY E:51 , GLY E:52 , TRP E:164 , TYR E:165 , ALA E:166 , ALA E:201 , THR E:202 , GLY E:203 , THR E:213 , ASN E:214 , ASP E:221 , LEU E:252 , HIS E:354 , TYR E:355 , GLY E:387 , GLU E:388 , ARG E:399 , GLY E:402 , ASN E:403 , SER E:404 , LEU E:405 , LEU E:408 , TEO E:1589 , HOH E:2015
BINDING SITE FOR RESIDUE FAD E 601
2
AC7
SOFTWARE
CYS F:55 , ARG F:56 , GLY F:58 , VAL F:59 , CYS F:60 , GLY F:61 , ASP F:63 , CYS F:75
BINDING SITE FOR RESIDUE FES F 302
3
AC8
SOFTWARE
CYS F:149 , ILE F:150 , CYS F:152 , ALA F:153 , CYS F:154 , CYS F:155 , ALA F:173 , CYS F:216 , PRO F:217
BINDING SITE FOR RESIDUE SF4 F 303
4
AC9
SOFTWARE
CYS F:159 , PRO F:172 , CYS F:206 , HIS F:207 , SER F:208 , ILE F:209 , MET F:210 , ASN F:211 , CYS F:212 , THR F:223
BINDING SITE FOR RESIDUE F3S F 304
5
BC1
SOFTWARE
HIS F:207 , HIS G:30 , ARG G:31 , GLY G:34 , THR G:37 , PHE G:38 , HIS G:84 , VAL G:85 , GLY G:88 , HIS G:91 , CBE G:1130 , ARG H:20 , ALA H:23 , LEU H:26 , THR H:27 , MET H:71 , GLY H:75 , GLN H:78 , HOH H:2001
BINDING SITE FOR RESIDUE HEM G 305
6
BC8
SOFTWARE
TRP F:164 , PHE G:20 , SER G:27 , ILE G:28 , ARG G:31 , HEM G:305 , HOH G:2006 , ASP H:82 , TYR H:83
BINDING SITE FOR RESIDUE CBE G1130
7
CC1
SOFTWARE
GLY E:51 , PHE E:119 , HIS E:242 , THR E:254 , GLU E:255 , ARG E:286 , HIS E:354 , ARG E:399 , GLY E:401 , GLY E:402 , FAD E:601
BINDING SITE FOR RESIDUE TEO E1589
8
CC5
SOFTWARE
TYR E:355 , MET E:356 , MET E:357 , GLY E:358 , GLU E:388 , ALA E:390
BINDING SITE FOR RESIDUE NA E1590
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(6, 6)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (F:8-97)
2: SDH_CYT_1 (G:9-33)
3: FRD_SDH_FAD_BINDING (E:43-52)
4: SDH_CYT_2 (G:84-97)
5: 4FE4S_FER_2 (F:139-169)
6: 4FE4S_FER_1 (F:149-160)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
SDHB_ECOLI
8-97
1
-
F:8-97
-
2
SDH_CYT_1
PS01000
Succinate dehydrogenase cytochrome b subunit signature 1.
DHSC_ECOLI
9-33
1
-
G:9-33
-
3
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
SDHA_ECOLI
43-52
1
-
E:43-52
-
4
SDH_CYT_2
PS01001
Succinate dehydrogenase cytochrome b subunit signature 2.
DHSC_ECOLI
84-97
1
-
G:84-97
-
5
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
SDHB_ECOLI
139-169
1
-
F:139-169
-
6
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
SDHB_ECOLI
149-160
1
-
F:149-160
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(6, 18)
Info
All SCOP Domains
1a: SCOP_d2wu5b2 (B:107-238)
1b: SCOP_d2wu5f2 (F:107-238)
1c: SCOP_d2wu5j2 (J:107-238)
2a: SCOP_d2wu5a3 (A:451-588)
2b: SCOP_d2wu5e3 (E:451-588)
2c: SCOP_d2wu5i3 (I:451-588)
3a: SCOP_d2wu5b1 (B:1-106)
3b: SCOP_d2wu5f1 (F:1-106)
3c: SCOP_d2wu5j1 (J:1-106)
4a: SCOP_d2wu5a2 (A:236-355)
4b: SCOP_d2wu5e2 (E:236-355)
4c: SCOP_d2wu5i2 (I:236-355)
5a: SCOP_d2wu5a1 (A:1-235,A:356-450)
5b: SCOP_d2wu5e1 (E:1-235,E:356-450)
5c: SCOP_d2wu5i1 (I:1-235,I:356-450)
6a: SCOP_d2wu5c_ (C:)
6b: SCOP_d2wu5g_ (G:)
6c: SCOP_d2wu5k_ (K:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
alpha-helical ferredoxin
(43)
Family
:
Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
(35)
Protein domain
:
Succinate dehydogenase
(16)
Escherichia coli [TaxId: 562]
(5)
1a
d2wu5b2
B:107-238
1b
d2wu5f2
F:107-238
1c
d2wu5j2
J:107-238
Fold
:
Spectrin repeat-like
(186)
Superfamily
:
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
(26)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
(26)
Protein domain
:
Succinate dehydogenase
(11)
Escherichia coli [TaxId: 562]
(6)
2a
d2wu5a3
A:451-588
2b
d2wu5e3
E:451-588
2c
d2wu5i3
I:451-588
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Succinate dehydogenase iron-sulfur protein, N-terminal domain
(16)
Escherichia coli [TaxId: 562]
(5)
3a
d2wu5b1
B:1-106
3b
d2wu5f1
F:1-106
3c
d2wu5j1
J:1-106
Fold
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Superfamily
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
(45)
Protein domain
:
Succinate dehydogenase
(11)
Escherichia coli [TaxId: 562]
(6)
4a
d2wu5a2
A:236-355
4b
d2wu5e2
E:236-355
4c
d2wu5i2
I:236-355
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain
(45)
Protein domain
:
Succinate dehydogenase
(11)
Escherichia coli [TaxId: 562]
(6)
5a
d2wu5a1
A:1-235,A:356-450
5b
d2wu5e1
E:1-235,E:356-450
5c
d2wu5i1
I:1-235,I:356-450
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Fumarate reductase respiratory complex transmembrane subunits
(55)
Family
:
Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
(48)
Protein domain
:
Succinate dehydrogenase subunit SdhC
(7)
Escherichia coli [TaxId: 562]
(7)
6a
d2wu5c_
C:
6b
d2wu5g_
G:
6c
d2wu5k_
K:
[
close SCOP info
]
CATH Domains
(6, 21)
Info
all CATH domains
1a: CATH_2wu5A01 (A:1-245,A:351-430)
1b: CATH_2wu5E01 (E:1-245,E:351-430)
1c: CATH_2wu5I01 (I:1-245,I:351-430)
2a: CATH_2wu5B01 (B:1-106)
2b: CATH_2wu5F01 (F:1-106)
2c: CATH_2wu5J01 (J:1-106)
3a: CATH_2wu5A04 (A:548-588)
3b: CATH_2wu5E04 (E:548-588)
3c: CATH_2wu5I04 (I:548-588)
4a: CATH_2wu5B02 (B:107-238)
4b: CATH_2wu5F02 (F:107-238)
4c: CATH_2wu5J02 (J:107-238)
5a: CATH_2wu5C00 (C:8-129)
5b: CATH_2wu5D00 (D:11-115)
5c: CATH_2wu5H00 (H:11-115)
5d: CATH_2wu5L00 (L:11-115)
5e: CATH_2wu5G00 (G:8-129)
5f: CATH_2wu5K00 (K:8-129)
6a: CATH_2wu5A03 (A:431-547)
6b: CATH_2wu5E03 (E:431-547)
6c: CATH_2wu5I03 (I:431-547)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Escherichia coli. Organism_taxid: 562.
(12)
1a
2wu5A01
A:1-245,A:351-430
1b
2wu5E01
E:1-245,E:351-430
1c
2wu5I01
I:1-245,I:351-430
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Escherichia coli. Organism_taxid: 562.
(14)
2a
2wu5B01
B:1-106
2b
2wu5F01
F:1-106
2c
2wu5J01
J:1-106
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
succinate dehydrogenase protein domain
(23)
Escherichia coli. Organism_taxid: 562.
(10)
3a
2wu5A04
A:548-588
3b
2wu5E04
E:548-588
3c
2wu5I04
I:548-588
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Homologous Superfamily
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Escherichia coli. Organism_taxid: 562.
(10)
4a
2wu5B02
B:107-238
4b
2wu5F02
F:107-238
4c
2wu5J02
J:107-238
Architecture
:
Up-down Bundle
(3216)
Topology
:
3 helical TM bundles of succinate and fumarate reductases
(23)
Homologous Superfamily
:
Fumarate reductase respiratory complex transmembrane subunits
(23)
Escherichia coli. Organism_taxid: 562.
(10)
5a
2wu5C00
C:8-129
5b
2wu5D00
D:11-115
5c
2wu5H00
H:11-115
5d
2wu5L00
L:11-115
5e
2wu5G00
G:8-129
5f
2wu5K00
K:8-129
Topology
:
Methane Monooxygenase Hydroxylase; Chain G, domain 1
(192)
Homologous Superfamily
:
[code=1.20.58.100, no name defined]
(37)
Escherichia coli. Organism_taxid: 562.
(10)
6a
2wu5A03
A:431-547
6b
2wu5E03
E:431-547
6c
2wu5I03
I:431-547
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Sdh_cyt_2wu5K01 (K:8-124)
1b: PFAM_Sdh_cyt_2wu5K02 (K:8-124)
1c: PFAM_Sdh_cyt_2wu5K03 (K:8-124)
1d: PFAM_Sdh_cyt_2wu5L01 (L:11-113)
1e: PFAM_Sdh_cyt_2wu5L02 (L:11-113)
1f: PFAM_Sdh_cyt_2wu5L03 (L:11-113)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FumRed-TM
(17)
Family
:
Sdh_cyt
(10)
Escherichia coli (strain K12)
(8)
1a
Sdh_cyt-2wu5K01
K:8-124
1b
Sdh_cyt-2wu5K02
K:8-124
1c
Sdh_cyt-2wu5K03
K:8-124
1d
Sdh_cyt-2wu5L01
L:11-113
1e
Sdh_cyt-2wu5L02
L:11-113
1f
Sdh_cyt-2wu5L03
L:11-113
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (362 KB)
Header - Biol.Unit 1
Biol.Unit 2 (358 KB)
Header - Biol.Unit 2
Biol.Unit 3 (365 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2WU5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
