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2FYN
Biol. Unit 2
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Asym.Unit (867 KB)
Biol.Unit 1 (290 KB)
Biol.Unit 2 (290 KB)
Biol.Unit 3 (290 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF THE DOUBLE MUTANT RHODOBACTER SPHAEROIDES BC1 COMPLEX
Authors
:
L. Esser, D. Xia
Date
:
08 Feb 06 (Deposition) - 29 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: M,N,O,P,Q,R (1x)
Keywords
:
Transmembrane Helices, Functional Dimer, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Esser, X. Gong, S. Yang, L. Yu, C. A. Yu, D. Xia
Surface-Modulated Motion Switch: Capture And Release Of Iron-Sulfur Protein In The Cytochrome Bc1 Complex.
Proc. Natl. Acad. Sci. Usa V. 103 13045 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: FE2/S2 (INORGANIC) CLUSTER (FESa)
1b: FE2/S2 (INORGANIC) CLUSTER (FESb)
1c: FE2/S2 (INORGANIC) CLUSTER (FESc)
1d: FE2/S2 (INORGANIC) CLUSTER (FESd)
1e: FE2/S2 (INORGANIC) CLUSTER (FESe)
1f: FE2/S2 (INORGANIC) CLUSTER (FESf)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
2f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
2h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
2i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
2j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
2k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
2l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
2m: PROTOPORPHYRIN IX CONTAINING FE (HEMm)
2n: PROTOPORPHYRIN IX CONTAINING FE (HEMn)
2o: PROTOPORPHYRIN IX CONTAINING FE (HEMo)
2p: PROTOPORPHYRIN IX CONTAINING FE (HEMp)
2q: PROTOPORPHYRIN IX CONTAINING FE (HEMq)
2r: PROTOPORPHYRIN IX CONTAINING FE (HEMr)
3a: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPa)
3b: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPb)
3c: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPc)
3d: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPd)
3e: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPe)
3f: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPf)
4a: STIGMATELLIN A (SMAa)
4b: STIGMATELLIN A (SMAb)
4c: STIGMATELLIN A (SMAc)
4d: STIGMATELLIN A (SMAd)
4e: STIGMATELLIN A (SMAe)
4f: STIGMATELLIN A (SMAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
2
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
LOP
2
Ligand/Ion
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
4
SMA
2
Ligand/Ion
STIGMATELLIN A
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC9 (SOFTWARE)
02: BC1 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC5 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC6 (SOFTWARE)
12: DC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC9
SOFTWARE
TRP G:45 , GLY G:48 , LEU G:51 , ALA G:52 , VAL G:108 , HIS G:111 , ILE G:112 , ARG G:114 , ARG G:125 , THR G:128 , TRP G:129 , GLY G:132 , MET G:133 , ILE G:135 , TYR G:136 , VAL G:209 , HIS G:212 , PHE G:216 , ASN G:222
BINDING SITE FOR RESIDUE HEM G 501
02
BC1
SOFTWARE
GLN G:58 , GLY G:62 , ILE G:63 , VAL G:80 , ARG G:94 , HIS G:97 , THR G:142 , ALA G:143 , GLY G:146 , TYR G:147 , PRO G:150 , HIS G:198 , TYR G:199 , PRO G:202
BINDING SITE FOR RESIDUE HEM G 502
03
BC2
SOFTWARE
VAL H:35 , CYS H:36 , CYS H:39 , HIS H:40 , ASN H:96 , PRO H:98 , MET H:103 , ARG H:107 , TYR H:130 , ILE H:183 , ALA H:184 , MET H:185 , PRO H:188
BINDING SITE FOR RESIDUE HEM H 301
04
BC3
SOFTWARE
CYS I:129 , HIS I:131 , LEU I:132 , GLY I:133 , CYS I:134 , CYS I:149 , HIS I:152 , SER I:154
BINDING SITE FOR RESIDUE FES I 200
05
BC4
SOFTWARE
TRP J:45 , GLY J:48 , LEU J:51 , ALA J:52 , VAL J:108 , HIS J:111 , ARG J:114 , ARG J:125 , THR J:128 , TRP J:129 , GLY J:132 , MET J:133 , ILE J:135 , TYR J:136 , VAL J:209 , HIS J:212 , PHE J:216 , GLY J:220 , ASN J:222
BINDING SITE FOR RESIDUE HEM J 501
06
BC5
SOFTWARE
GLN J:58 , GLY J:62 , ILE J:63 , ARG J:94 , HIS J:97 , ALA J:101 , THR J:142 , GLY J:146 , TYR J:147 , PRO J:150 , HIS J:198 , TYR J:199 , PRO J:202
BINDING SITE FOR RESIDUE HEM J 502
07
BC6
SOFTWARE
VAL K:35 , CYS K:36 , CYS K:39 , HIS K:40 , ASN K:96 , PRO K:98 , MET K:103 , ARG K:107 , TYR K:130 , LEU K:135 , ILE K:183 , ALA K:184 , MET K:185 , PRO K:188
BINDING SITE FOR RESIDUE HEM K 301
08
BC7
SOFTWARE
CYS L:129 , HIS L:131 , LEU L:132 , GLY L:133 , CYS L:134 , CYS L:149 , HIS L:152 , SER L:154
BINDING SITE FOR RESIDUE FES L 200
09
CC9
SOFTWARE
PHE G:144 , GLY G:158 , VAL G:161 , ILE G:162 , PHE G:194 , ILE G:292 , VAL G:293 , PRO G:294 , GLU G:295 , PHE G:298 , TYR G:302 , PHE G:337 , HIS L:152
BINDING SITE FOR RESIDUE SMA G 503
10
DC1
SOFTWARE
CYS I:151 , HIS I:152 , MET J:140 , PHE J:144 , GLY J:158 , VAL J:161 , ILE J:162 , ILE J:292 , VAL J:293 , PRO J:294 , GLU J:295 , PHE J:298 , TYR J:302 , MET J:336
BINDING SITE FOR RESIDUE SMA J 503
11
DC6
SOFTWARE
MET G:44 , TRP G:47 , ASN G:99 , LEU G:103 , ILE G:106 , PHE G:113 , TYR G:117 , TYR G:118 , ARG G:358
BINDING SITE FOR RESIDUE LOP G 504
12
DC7
SOFTWARE
MET J:44 , PHE J:113 , TYR J:117 , TYR J:118 , VAL J:262 , PHE J:263 , ARG J:358 , PHE J:374
BINDING SITE FOR RESIDUE LOP J 504
[
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
(4, 8)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (G:15-225,J:15-225)
2: CYTC (H:23-142,K:23-142)
3: RIESKE (I:117-185,L:117-185)
4: CYTB_CTER (G:234-422,J:234-422)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTB_NTER
PS51002
Cytochrome b/b6 N-terminal region profile.
CYB_RHOSH
15-225
2
-
-
G:15-225
J:15-225
-
-
2
CYTC
PS51007
Cytochrome c family profile.
CY1_RHOSH
45-164
2
-
-
H:23-142
K:23-142
-
-
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_RHOSH
117-185
2
-
-
I:117-185
L:117-185
-
-
4
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_RHOSH
234-422
2
-
-
G:234-422
J:234-422
-
-
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(5, 30)
Info
all CATH domains
1a: CATH_2fynB01 (B:1-221)
1b: CATH_2fynE01 (E:1-221)
1c: CATH_2fynH01 (H:1-221)
1d: CATH_2fynK01 (K:1-221)
1e: CATH_2fynN01 (N:1-221)
1f: CATH_2fynQ01 (Q:1-221)
2a: CATH_2fynA00 (A:3-430)
2b: CATH_2fynD00 (D:3-430)
2c: CATH_2fynG00 (G:3-430)
2d: CATH_2fynJ00 (J:3-430)
2e: CATH_2fynM00 (M:3-430)
2f: CATH_2fynP00 (P:3-430)
3a: CATH_2fynB02 (B:222-256)
3b: CATH_2fynN02 (N:222-256)
3c: CATH_2fynQ02 (Q:222-256)
3d: CATH_2fynE02 (E:222-256)
3e: CATH_2fynH02 (H:222-256)
3f: CATH_2fynK02 (K:222-256)
4a: CATH_2fynC01 (C:9-41)
4b: CATH_2fynF01 (F:9-41)
4c: CATH_2fynI01 (I:9-41)
4d: CATH_2fynL01 (L:9-41)
4e: CATH_2fynO01 (O:9-41)
4f: CATH_2fynR01 (R:9-41)
5a: CATH_2fynC02 (C:42-187)
5b: CATH_2fynF02 (F:42-187)
5c: CATH_2fynI02 (I:42-187)
5d: CATH_2fynL02 (L:42-187)
5e: CATH_2fynO02 (O:42-187)
5f: CATH_2fynR02 (R:42-187)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
1a
2fynB01
B:1-221
1b
2fynE01
E:1-221
1c
2fynH01
H:1-221
1d
2fynK01
K:1-221
1e
2fynN01
N:1-221
1f
2fynQ01
Q:1-221
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
2a
2fynA00
A:3-430
2b
2fynD00
D:3-430
2c
2fynG00
G:3-430
2d
2fynJ00
J:3-430
2e
2fynM00
M:3-430
2f
2fynP00
P:3-430
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.100, no name defined]
(56)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
3a
2fynB02
B:222-256
3b
2fynN02
N:222-256
3c
2fynQ02
Q:222-256
3d
2fynE02
E:222-256
3e
2fynH02
H:222-256
3f
2fynK02
K:222-256
Homologous Superfamily
:
Single helix bin
(16)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
4a
2fynC01
C:9-41
4b
2fynF01
F:9-41
4c
2fynI01
I:9-41
4d
2fynL01
L:9-41
4e
2fynO01
O:9-41
4f
2fynR01
R:9-41
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(10)
5a
2fynC02
C:42-187
5b
2fynF02
F:42-187
5c
2fynI02
I:42-187
5d
2fynL02
L:42-187
5e
2fynO02
O:42-187
5f
2fynR02
R:42-187
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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