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3DTU
Asym. Unit
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
)
[
close entry info
]
Hetero Components
(11, 57)
Info
All Hetero Components
01a: CALCIUM ION (CAa)
01b: CALCIUM ION (CAb)
02a: CADMIUM ION (CDa)
02b: CADMIUM ION (CDb)
02c: CADMIUM ION (CDc)
02d: CADMIUM ION (CDd)
02e: CADMIUM ION (CDe)
03a: COPPER (II) ION (CUa)
03b: COPPER (II) ION (CUb)
03c: COPPER (II) ION (CUc)
03d: COPPER (II) ION (CUd)
03e: COPPER (II) ION (CUe)
03f: COPPER (II) ION (CUf)
04a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
04b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
04c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
04d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
04e: DECYL-BETA-D-MALTOPYRANOSIDE (DMUe)
04f: DECYL-BETA-D-MALTOPYRANOSIDE (DMUf)
04g: DECYL-BETA-D-MALTOPYRANOSIDE (DMUg)
04h: DECYL-BETA-D-MALTOPYRANOSIDE (DMUh)
04i: DECYL-BETA-D-MALTOPYRANOSIDE (DMUi)
05a: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDR... (DXCa)
06a: HEME-A (HEAa)
06b: HEME-A (HEAb)
06c: HEME-A (HEAc)
06d: HEME-A (HEAd)
07a: HEPTANE-1,2,3-TRIOL (HTOa)
08a: MAGNESIUM ION (MGa)
08b: MAGNESIUM ION (MGb)
09a: HYDROXIDE ION (OHa)
09b: 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
2
Ligand/Ion
CALCIUM ION
2
CD
5
Ligand/Ion
CADMIUM ION
3
CU
6
Ligand/Ion
COPPER (II) ION
4
DMU
9
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
DXC
1
Ligand/Ion
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OICACID
6
HEA
4
Ligand/Ion
HEME-A
7
HTO
1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
8
MG
2
Ligand/Ion
MAGNESIUM ION
9
OH
2
Ligand/Ion
HYDROXIDE ION
10
PO4
2
Ligand/Ion
PHOSPHATE ION
11
TRD
23
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(44, 44)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (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
AC6
SOFTWARE
MET C:56 , GLN C:61 , PHE C:62 , SER C:83 , PHE C:505 , HOH C:642 , HOH C:684
BINDING SITE FOR RESIDUE DMU C 567
07
AC7
SOFTWARE
GLU A:86 , PRO B:174 , TYR C:318 , HOH C:718 , HOH C:752
BINDING SITE FOR RESIDUE DMU C 568
08
AC8
SOFTWARE
PRO D:121 , PHE D:124 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 11
09
AC9
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , HOH A:1511
BINDING SITE FOR RESIDUE CU A 1023
10
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
11
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
12
BC3
SOFTWARE
HIS A:284 , HIS A:334 , HOH A:1511
BINDING SITE FOR RESIDUE OH A 1501
13
BC4
SOFTWARE
PHE A:135 , PRO A:136 , ARG A:137 , MET A:138
BINDING SITE FOR RESIDUE PO4 A 1001
14
BC5
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260
BINDING SITE FOR RESIDUE CU B 1022
15
BC6
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263
BINDING SITE FOR RESIDUE CU B 1004
16
BC7
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 1008
17
BC8
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:1157 , HOH B:1158
BINDING SITE FOR RESIDUE CD B 1009
18
BC9
SOFTWARE
HIS B:284 , HIS B:286 , HOH B:1162 , HOH B:1176
BINDING SITE FOR RESIDUE CD B 1010
19
CC1
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334
BINDING SITE FOR RESIDUE CU C 569
20
CC2
SOFTWARE
HIS C:411 , ASP C:412 , HOH C:628 , GLU D:254 , HOH D:321 , HOH D:333
BINDING SITE FOR RESIDUE MG C 570
21
CC3
SOFTWARE
GLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:629 , HOH C:642
BINDING SITE FOR RESIDUE CA C 571
22
CC4
SOFTWARE
HIS C:284 , HIS C:334 , HOH C:589
BINDING SITE FOR RESIDUE OH C 572
23
CC5
SOFTWARE
PHE C:135 , PRO C:136 , ARG C:137 , MET C:138
BINDING SITE FOR RESIDUE PO4 C 573
24
CC6
SOFTWARE
CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260
BINDING SITE FOR RESIDUE CU D 3
25
CC7
SOFTWARE
HIS D:217 , CYS D:252 , CYS D:256 , MET D:263
BINDING SITE FOR RESIDUE CU D 4
26
CC8
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 8
27
CC9
SOFTWARE
HOH C:719 , HIS D:96 , GLU D:101
BINDING SITE FOR RESIDUE CD D 9
28
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
29
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
30
DC3
SOFTWARE
TRP A:451 , GLY A:513 , TYR A:517
BINDING SITE FOR RESIDUE TRD A 1504
31
DC4
SOFTWARE
LEU A:80 , TRP A:81
BINDING SITE FOR RESIDUE TRD A 1505
32
DC5
SOFTWARE
ARG A:476 , THR B:41 , GLY B:42
BINDING SITE FOR RESIDUE TRD A 1506
33
DC6
SOFTWARE
PHE A:76 , SER A:79
BINDING SITE FOR RESIDUE TRD A 1013
34
DC7
SOFTWARE
PHE B:71
BINDING SITE FOR RESIDUE TRD B 1012
35
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
36
DC9
SOFTWARE
LEU C:34 , THR C:48 , MET C:51 , ARG C:52 , TRP C:95 , ILE C:99 , HIS C:102 , MET C:106 , MET C:107 , GLY C:171 , TRP C:172 , TYR C:414 , PHE C:420 , HIS C:421 , MET C:424 , SER C:425 , PHE C:468 , GLN C:471 , ARG C:481 , ARG C:482 , SER C:504 , PHE C:508 , HOH C:585 , HOH C:587 , HOH C:652
BINDING SITE FOR RESIDUE HEA C 574
37
EC1
SOFTWARE
TRP C:172 , TRP C:280 , TYR C:288 , HIS C:333 , THR C:352 , ILE C:355 , THR C:359 , GLY C:360 , GLY C:395 , GLY C:398 , ILE C:399 , LEU C:401 , SER C:402 , ASP C:407 , HIS C:411 , HIS C:419 , PHE C:420 , MET C:424 , ARG C:481 , HOH C:589 , HOH C:598 , HOH C:605 , HOH C:614 , HOH C:635
BINDING SITE FOR RESIDUE HEA C 575
38
EC2
SOFTWARE
PRO C:315 , TYR C:318 , ALA C:319 , ALA C:322 , PRO C:358 , ILE C:361 , HOH C:718 , HOH C:720 , HOH C:721 , HIS D:96 , GLU D:101
BINDING SITE FOR RESIDUE DXC C 576
39
EC3
SOFTWARE
MET C:443 , SER C:444
BINDING SITE FOR RESIDUE TRD C 577
40
EC4
SOFTWARE
TYR C:50 , PHE C:76
BINDING SITE FOR RESIDUE TRD C 579
41
EC5
SOFTWARE
HIS C:223 , LYS C:224 , ASP C:536
BINDING SITE FOR RESIDUE TRD C 583
42
EC6
SOFTWARE
HIS C:127 , HIS C:300 , ALA C:303 , THR C:304 , PHE C:438 , HIS C:534 , ALA C:535 , ASP C:536 , THR C:537 , GLU C:539 , TRP C:540 , HOH C:686 , HOH C:701
BINDING SITE FOR RESIDUE TRD C 584
43
EC7
SOFTWARE
ARG C:476 , THR D:41 , GLY D:42 , THR D:69
BINDING SITE FOR RESIDUE TRD D 7
44
EC8
SOFTWARE
PHE D:71
BINDING SITE FOR RESIDUE TRD D 12
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(5, 10)
Info
All PROSITE Patterns/Profiles
1: COX1 (A:20-551,C:20-552)
2: COX2_TM (B:35-130,D:35-130)
3: COX2_CUA (B:131-281,D:131-281)
4: COX2 (B:215-263,D:215-263)
5: COX1_CUB (A:280-334,C:280-334)
;
View:
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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
2
A:20-551
C:20-552
2
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_RHOSH
35-130
2
B:35-130
D:35-130
3
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_RHOSH
131-281
2
B:131-281
D:131-281
4
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_RHOSH
215-263
2
B:215-263
D:215-263
5
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_RHOSH
280-334
2
A:280-334
C:280-334
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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Folds
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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
[
close SCOP info
]
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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(
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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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Sorry, no Info available
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (294 KB)
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