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3DTU
Biol. Unit 1
Info
Asym.Unit (294 KB)
Biol.Unit 1 (144 KB)
Biol.Unit 2 (143 KB)
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(1)
Title
:
CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES COMPLEXED WITH DEOXYCHOLIC ACID
Authors
:
L. Qin, D. A. Mills, L. Buhrow, C. Hiser, S. Ferguson-Miller
Date
:
15 Jul 08 (Deposition) - 16 Sep 08 (Release) - 24 Feb 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
:
Transmembrane Protein Complex, Deoxycholic Acid, Copper, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Qin, D. A. Mills, L. Buhrow, C. Hiser, S. Ferguson-Miller
A Conserved Steroid Binding Site In Cytochrome C Oxidase.
Biochemistry V. 47 9931 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 21)
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)
2e: CADMIUM ION (CDe)
3a: COPPER (II) ION (CUa)
3b: COPPER (II) ION (CUb)
3c: COPPER (II) ION (CUc)
3d: COPPER (II) ION (CUd)
3e: COPPER (II) ION (CUe)
3f: COPPER (II) ION (CUf)
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)
5a: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCa)
6a: HEME-A (HEAa)
6b: HEME-A (HEAb)
6c: HEME-A (HEAc)
6d: HEME-A (HEAd)
7a: HEPTANE-1,2,3-TRIOL (HTOa)
8a: MAGNESIUM ION (MGa)
8b: MAGNESIUM ION (MGb)
9a: HYDROXIDE ION (OHa)
9b: HYDROXIDE ION (OHb)
10a: PHOSPHATE ION (PO4a)
10b: PHOSPHATE ION (PO4b)
11a: TRIDECANE (TRDa)
11b: TRIDECANE (TRDb)
11c: TRIDECANE (TRDc)
11d: TRIDECANE (TRDd)
11e: TRIDECANE (TRDe)
11f: TRIDECANE (TRDf)
11g: TRIDECANE (TRDg)
11h: TRIDECANE (TRDh)
11i: TRIDECANE (TRDi)
11j: TRIDECANE (TRDj)
11k: TRIDECANE (TRDk)
11l: TRIDECANE (TRDl)
11m: TRIDECANE (TRDm)
11n: TRIDECANE (TRDn)
11o: TRIDECANE (TRDo)
11p: TRIDECANE (TRDp)
11q: TRIDECANE (TRDq)
11r: TRIDECANE (TRDr)
11s: TRIDECANE (TRDs)
11t: TRIDECANE (TRDt)
11u: TRIDECANE (TRDu)
11v: TRIDECANE (TRDv)
11w: TRIDECANE (TRDw)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
CU
-1
Ligand/Ion
COPPER (II) ION
4
DMU
6
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
DXC
-1
Ligand/Ion
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OICACID
6
HEA
2
Ligand/Ion
HEME-A
7
HTO
1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
8
MG
-1
Ligand/Ion
MAGNESIUM ION
9
OH
-1
Ligand/Ion
HYDROXIDE ION
10
PO4
1
Ligand/Ion
PHOSPHATE ION
11
TRD
11
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC8 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC3 (SOFTWARE)
21: DC4 (SOFTWARE)
22: DC5 (SOFTWARE)
23: DC6 (SOFTWARE)
24: DC7 (SOFTWARE)
25: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:83 , ALA A:84 , ASN A:87 , HOH A:1636 , TRP C:371 , LEU D:75 , PHE D:94 , HIS D:96 , ASN D:97
BINDING SITE FOR RESIDUE DMU A 567
02
AC2
SOFTWARE
TRP A:20 , MET A:443 , LEU A:512 , HOH A:1560
BINDING SITE FOR RESIDUE DMU A 1004
03
AC3
SOFTWARE
MET A:56 , ALA A:57 , GLN A:61 , SER A:83 , PHE A:502 , PHE A:505 , HOH A:1563 , HOH A:1606
BINDING SITE FOR RESIDUE DMU A 1005
04
AC4
SOFTWARE
TRP A:371 , HIS B:96 , ASN B:97
BINDING SITE FOR RESIDUE DMU B 1003
05
AC5
SOFTWARE
PRO B:121 , GLU B:128 , HOH B:1182
BINDING SITE FOR RESIDUE DMU B 1011
06
AC7
SOFTWARE
GLU A:86 , PRO B:174 , TYR C:318 , HOH C:718 , HOH C:752
BINDING SITE FOR RESIDUE DMU C 568
07
AC9
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , HOH A:1511
BINDING SITE FOR RESIDUE CU A 1023
08
BC1
SOFTWARE
HIS A:411 , ASP A:412 , GLU B:254 , HOH B:1064 , HOH B:1070 , HOH B:1077
BINDING SITE FOR RESIDUE MG A 1006
09
BC2
SOFTWARE
GLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:1550 , HOH A:1563
BINDING SITE FOR RESIDUE CA A 1007
10
BC3
SOFTWARE
HIS A:284 , HIS A:334 , HOH A:1511
BINDING SITE FOR RESIDUE OH A 1501
11
BC4
SOFTWARE
PHE A:135 , PRO A:136 , ARG A:137 , MET A:138
BINDING SITE FOR RESIDUE PO4 A 1001
12
BC5
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260
BINDING SITE FOR RESIDUE CU B 1022
13
BC6
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263
BINDING SITE FOR RESIDUE CU B 1004
14
BC7
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 1008
15
BC8
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:1157 , HOH B:1158
BINDING SITE FOR RESIDUE CD B 1009
16
BC9
SOFTWARE
HIS B:284 , HIS B:286 , HOH B:1162 , HOH B:1176
BINDING SITE FOR RESIDUE CD B 1010
17
CC8
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 8
18
DC1
SOFTWARE
LEU A:34 , THR A:48 , MET A:51 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , MET A:106 , MET A:107 , GLY A:171 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , MET A:424 , SER A:425 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , HOH A:1507 , HOH A:1509 , HOH A:1573
BINDING SITE FOR RESIDUE HEA A 1502
19
DC2
SOFTWARE
TRP A:172 , TRP A:280 , TYR A:288 , HIS A:333 , HIS A:334 , THR A:352 , ILE A:355 , THR A:359 , GLY A:360 , GLY A:395 , GLY A:398 , LEU A:401 , SER A:402 , ASP A:407 , HIS A:411 , HIS A:419 , PHE A:420 , MET A:424 , ARG A:481 , HOH A:1511 , HOH A:1520 , HOH A:1527 , HOH A:1536 , HOH A:1556
BINDING SITE FOR RESIDUE HEA A 1503
20
DC3
SOFTWARE
TRP A:451 , GLY A:513 , TYR A:517
BINDING SITE FOR RESIDUE TRD A 1504
21
DC4
SOFTWARE
LEU A:80 , TRP A:81
BINDING SITE FOR RESIDUE TRD A 1505
22
DC5
SOFTWARE
ARG A:476 , THR B:41 , GLY B:42
BINDING SITE FOR RESIDUE TRD A 1506
23
DC6
SOFTWARE
PHE A:76 , SER A:79
BINDING SITE FOR RESIDUE TRD A 1013
24
DC7
SOFTWARE
PHE B:71
BINDING SITE FOR RESIDUE TRD B 1012
25
DC8
SOFTWARE
ALA B:276 , GLU B:280 , HIS B:283 , HOH B:1160 , HOH B:1178 , GLU D:152 , ALA D:276 , GLU D:280 , HIS D:283 , HOH D:298
BINDING SITE FOR RESIDUE HTO B 1
[
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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 (A:20-551)
2: COX2_TM (B:35-130)
3: COX2_CUA (B:131-281)
4: COX2 (B:215-263)
5: COX1_CUB (A: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
A:20-551
-
2
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_RHOSH
35-130
1
B:35-130
-
3
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_RHOSH
131-281
1
B:131-281
-
4
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_RHOSH
215-263
1
B:215-263
-
5
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_RHOSH
280-334
1
A: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_d3dtub1 (B:130-287)
1b: SCOP_d3dtud1 (D:130-285)
2a: SCOP_d3dtua_ (A:)
2b: SCOP_d3dtuc_ (C:)
3a: SCOP_d3dtub2 (B:29-129)
3b: SCOP_d3dtud2 (D:28-129)
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Classes
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)
(
)
Folds
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)
(
)
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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
d3dtub1
B:130-287
1b
d3dtud1
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
d3dtua_
A:
2b
d3dtuc_
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
d3dtub2
B:29-129
3b
d3dtud2
D:28-129
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3dtuB01 (B:35-130)
1b: CATH_3dtuD01 (D:35-130)
2a: CATH_3dtuC00 (C:17-552)
2b: CATH_3dtuA00 (A:13-551)
3a: CATH_3dtuB02 (B:131-283)
3b: CATH_3dtuD02 (D:131-283)
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Topologies
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)
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
3dtuB01
B:35-130
1b
3dtuD01
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
3dtuC00
C:17-552
2b
3dtuA00
A:13-551
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
3a
3dtuB02
B:131-283
3b
3dtuD02
D:131-283
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (294 KB)
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