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3FYE
Biol. Unit 2
Info
Asym.Unit (288 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (140 KB)
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(1)
Title
:
CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES IN THE REDUCED STATE
Authors
:
L. Qin, D. A. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller
Date
:
22 Jan 09 (Deposition) - 16 Jun 09 (Release) - 16 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Conformational Changes, Cell Membrane, Copper, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Respiratory Chain, Transmembrane, Transport, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Qin, J. Liu, D. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller
Redox Dependent Conformational Changes In Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake.
Biochemistry V. 48 5121 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
3a: COPPER (I) ION (CU1a)
3b: COPPER (I) ION (CU1b)
3c: COPPER (I) ION (CU1c)
3d: COPPER (I) ION (CU1d)
3e: COPPER (I) ION (CU1e)
3f: COPPER (I) ION (CU1f)
4a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
4b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
4c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
4d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
4e: DECYL-BETA-D-MALTOPYRANOSIDE (DMUe)
4f: DECYL-BETA-D-MALTOPYRANOSIDE (DMUf)
4g: DECYL-BETA-D-MALTOPYRANOSIDE (DMUg)
4h: DECYL-BETA-D-MALTOPYRANOSIDE (DMUh)
4i: DECYL-BETA-D-MALTOPYRANOSIDE (DMUi)
4j: DECYL-BETA-D-MALTOPYRANOSIDE (DMUj)
5a: HEME-A (HEAa)
5b: HEME-A (HEAb)
5c: HEME-A (HEAc)
5d: HEME-A (HEAd)
6a: HEPTANE-1,2,3-TRIOL (HTOa)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
8a: TRIDECANE (TRDa)
8b: TRIDECANE (TRDb)
8c: TRIDECANE (TRDc)
8d: TRIDECANE (TRDd)
8e: TRIDECANE (TRDe)
8f: TRIDECANE (TRDf)
8g: TRIDECANE (TRDg)
8h: TRIDECANE (TRDh)
8i: TRIDECANE (TRDi)
8j: TRIDECANE (TRDj)
8k: TRIDECANE (TRDk)
8l: TRIDECANE (TRDl)
9a: UNKNOWN ATOM OR ION (UNXa)
9b: UNKNOWN ATOM OR ION (UNXb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
CU1
3
Ligand/Ion
COPPER (I) ION
4
DMU
4
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
HEA
2
Ligand/Ion
HEME-A
6
HTO
-1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
MG
-1
Ligand/Ion
MAGNESIUM ION
8
TRD
6
Ligand/Ion
TRIDECANE
9
UNX
1
Ligand/Ion
UNKNOWN ATOM OR ION
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: BC3 (SOFTWARE)
02: BC6 (SOFTWARE)
03: BC8 (SOFTWARE)
04: CC2 (SOFTWARE)
05: CC3 (SOFTWARE)
06: CC4 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC8 (SOFTWARE)
11: CC9 (SOFTWARE)
12: DC1 (SOFTWARE)
13: DC2 (SOFTWARE)
14: DC3 (SOFTWARE)
15: DC4 (SOFTWARE)
16: DC5 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC7 (SOFTWARE)
19: DC8 (SOFTWARE)
20: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC3
SOFTWARE
GLU B:152 , ALA B:276 , GLU B:280 , HIS B:283 , HOH B:292 , ALA D:276 , GLU D:280 , HIS D:283 , HOH D:1327
BINDING SITE FOR RESIDUE HTO B 1
02
BC6
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 8
03
BC8
SOFTWARE
TRP A:371 , PHE B:94 , HIS B:96 , ASN B:97 , LEU B:100 , TRP B:104 , GLU C:86 , PRO D:174 , GLU D:177 , HOH D:1151
BINDING SITE FOR RESIDUE DMU B 288
04
CC2
SOFTWARE
LEU C:34 , GLY C:38 , VAL C:45 , THR C:48 , MET C:51 , ARG C:52 , TRP C:95 , ILE C:99 , HIS C:102 , MET C:106 , MET C:107 , VAL C:111 , GLY C:171 , TRP C:172 , TYR C:414 , PHE C:420 , HIS C:421 , SER C:425 , VAL C:429 , MET C:460 , PHE C:468 , GLN C:471 , ARG C:482 , SER C:504 , PHE C:508 , HOH C:1003 , HOH C:1011 , HOH C:1130
BINDING SITE FOR RESIDUE HEA C 567
05
CC3
SOFTWARE
TRP C:172 , VAL C:287 , VAL C:291 , HIS C:333 , HIS C:334 , ALA C:356 , GLY C:360 , PHE C:364 , PHE C:391 , GLY C:395 , VAL C:396 , GLY C:398 , ILE C:399 , LEU C:401 , SER C:402 , ASP C:407 , HIS C:411 , VAL C:416 , HIS C:419 , PHE C:420 , VAL C:423 , MET C:424 , ARG C:481 , HOH C:1015 , HOH C:1030 , HOH C:1096 , HOH C:1371 , HOH C:1601 , HOH C:1603
BINDING SITE FOR RESIDUE HEA C 568
06
CC4
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334
BINDING SITE FOR RESIDUE CU1 C 570
07
CC5
SOFTWARE
HIS C:411 , ASP C:412 , HOH C:1082 , GLU D:254 , HOH D:1071 , HOH D:1094
BINDING SITE FOR RESIDUE MG C 571
08
CC6
SOFTWARE
GLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:1085 , HOH C:1107
BINDING SITE FOR RESIDUE CA C 572
09
CC7
SOFTWARE
TRP C:451 , GLY C:513 , TYR C:517 , DMU C:1002
BINDING SITE FOR RESIDUE TRD C 1001
10
CC8
SOFTWARE
TRP C:451 , TRD C:1001
BINDING SITE FOR RESIDUE DMU C 1002
11
CC9
SOFTWARE
MET C:56 , ALA C:57 , GLN C:61 , SER C:83 , VAL C:85 , PHE C:502 , PHE C:505 , TRD C:1006 , HOH C:1107
BINDING SITE FOR RESIDUE DMU C 1005
12
DC1
SOFTWARE
LEU C:80 , TRP C:81 , DMU C:1005
BINDING SITE FOR RESIDUE TRD C 1006
13
DC2
SOFTWARE
CU1 D:4 , CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260
BINDING SITE FOR RESIDUE CU1 D 3
14
DC3
SOFTWARE
CU1 D:3 , HIS D:217 , CYS D:252 , CYS D:256 , MET D:263
BINDING SITE FOR RESIDUE CU1 D 4
15
DC4
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 8
16
DC5
SOFTWARE
HIS D:96 , GLU D:101 , HOH D:1196 , HOH D:1805
BINDING SITE FOR RESIDUE CD D 9
17
DC6
SOFTWARE
TRP C:371 , PHE D:71 , LEU D:75 , PHE D:94 , HIS D:96 , ASN D:97 , TRP D:104
BINDING SITE FOR RESIDUE DMU D 1003
18
DC7
SOFTWARE
ARG C:476 , THR D:41
BINDING SITE FOR RESIDUE TRD D 1007
19
DC8
SOFTWARE
MET C:350
BINDING SITE FOR RESIDUE TRD D 1008
20
DC9
SOFTWARE
PRO D:121 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 1011
[
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]
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
[
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]
PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: COX1 (C:20-550)
2: COX2_TM (D:35-130)
3: COX2_CUA (D:131-281)
4: COX2 (D:215-263)
5: COX1_CUB (C:280-334)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX1
PS50855
Cytochrome oxidase subunit I profile.
COX1_RHOSH
20-558
1
-
C:20-550
2
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_RHOSH
35-130
1
-
D:35-130
3
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_RHOSH
131-281
1
-
D:131-281
4
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_RHOSH
215-263
1
-
D:215-263
5
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_RHOSH
280-334
1
-
C:280-334
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3fyeb2 (B:130-285)
1b: SCOP_d3fyed2 (D:130-285)
2a: SCOP_d3fyea_ (A:)
2b: SCOP_d3fyec_ (C:)
3a: SCOP_d3fyeb1 (B:30-129)
3b: SCOP_d3fyed1 (D:30-129)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Periplasmic domain of cytochrome c oxidase subunit II
(70)
Protein domain
:
Cytochrome c oxidase
(62)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
1a
d3fyeb2
B:130-285
1b
d3fyed2
D:130-285
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Cytochrome c oxidase subunit I-like
(65)
Superfamily
:
Cytochrome c oxidase subunit I-like
(65)
Family
:
Cytochrome c oxidase subunit I-like
(65)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit I
(8)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
2a
d3fyea_
A:
2b
d3fyec_
C:
Fold
:
Transmembrane helix hairpin
(84)
Superfamily
:
Cytochrome c oxidase subunit II-like, transmembrane region
(66)
Family
:
Cytochrome c oxidase subunit II-like, transmembrane region
(57)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit II
(10)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
3a
d3fyeb1
B:30-129
3b
d3fyed1
D:30-129
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3fyeB01 (B:35-130)
1b: CATH_3fyeD01 (D:35-130)
2a: CATH_3fyeC00 (C:20-550)
2b: CATH_3fyeA00 (A:17-551)
3a: CATH_3fyeB02 (B:131-283)
3b: CATH_3fyeD02 (D:131-283)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.90, no name defined]
(33)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
1a
3fyeB01
B:35-130
1b
3fyeD01
D:35-130
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
2a
3fyeC00
C:20-550
2b
3fyeA00
A:17-551
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
3a
3fyeB02
B:131-283
3b
3fyeD02
D:131-283
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (288 KB)
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