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2GSM
Biol. Unit 1
Info
Asym.Unit (288 KB)
Biol.Unit 1 (141 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
Authors
:
L. Qin, C. Hiser, A. Mulichak, R. M. Garavito, S. Ferguson-Miller
Date
:
26 Apr 06 (Deposition) - 10 Oct 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Transmembrane Protein Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Qin, C. Hiser, A. Mulichak, R. M. Garavito, S. Ferguson-Miller
Identification Of Conserved Lipid/Detergent-Binding Sites I A High-Resolution Structure Of The Membrane Protein Cytochrome C Oxidase.
Proc. Natl. Acad. Sci. Usa V. 103 16117 2006
[
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Hetero Components
(3, 13)
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 (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)
4j: DECYL-BETA-D-MALTOPYRANOSIDE (DMUj)
5a: HEME-A (HEAa)
5b: HEME-A (HEAb)
5c: HEME-A (HEAc)
5d: HEME-A (HEAd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
7a: HYDROXIDE ION (OHa)
7b: HYDROXIDE ION (OHb)
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)
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
5
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
HEA
2
Ligand/Ion
HEME-A
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
OH
-1
Ligand/Ion
HYDROXIDE ION
8
TRD
6
Ligand/Ion
TRIDECANE
[
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]
Sites
(21, 21)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC7 (SOFTWARE)
15: CC9 (SOFTWARE)
16: DC1 (SOFTWARE)
17: DC4 (SOFTWARE)
18: DC5 (SOFTWARE)
19: DC6 (SOFTWARE)
20: DC7 (SOFTWARE)
21: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:451 , PHE A:510 , TYR A:517 , DMU A:5002 , GLN B:142 , TRP B:143 , PRO B:164 , HOH B:5017 , HOH B:5033 , HOH B:5040 , HOH B:5125
BINDING SITE FOR RESIDUE DMU A 5001
02
AC2
SOFTWARE
TRP A:451 , ALA A:506 , DMU A:5001 , HOH A:6627
BINDING SITE FOR RESIDUE DMU A 5002
03
AC3
SOFTWARE
TRP A:371 , PHE B:94 , HIS B:96 , ASN B:97 , LEU B:100 , TRP B:104 , HOH B:5144 , GLU C:86 , SER D:173 , PRO D:174 , GLU D:177 , HOH D:1151
BINDING SITE FOR RESIDUE DMU B 5003
04
AC4
SOFTWARE
MET A:443 , SER A:444 , HOH A:6557
BINDING SITE FOR RESIDUE DMU A 5004
05
AC5
SOFTWARE
PHE B:124 , GLU B:128 , HOH B:5146
BINDING SITE FOR RESIDUE DMU B 5011
06
BC2
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260 , CU B:3004
BINDING SITE FOR RESIDUE CU B 3003
07
BC3
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263 , CU B:3003
BINDING SITE FOR RESIDUE CU B 3004
08
BC4
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , OH A:6501 , HOH A:6506
BINDING SITE FOR RESIDUE CU A 3005
09
BC5
SOFTWARE
HIS A:411 , ASP A:412 , GLU B:254 , HOH B:5042 , HOH B:5048 , HOH B:5055
BINDING SITE FOR RESIDUE MG A 3006
10
BC6
SOFTWARE
GLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:6547 , HOH A:6559
BINDING SITE FOR RESIDUE CA A 3007
11
BC7
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 3008
12
BC8
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:5113 , HOH B:5114
BINDING SITE FOR RESIDUE CD B 3009
13
CC5
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 4008
14
CC7
SOFTWARE
HIS A:284 , VAL A:287 , HIS A:334 , HEA A:2002 , CU A:3005 , HOH A:6506
BINDING SITE FOR RESIDUE OH A 6501
15
CC9
SOFTWARE
LEU A:34 , GLY A:38 , THR A:48 , MET A:51 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , MET A:106 , GLY A:171 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , SER A:425 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , HOH A:6502 , HOH A:6504 , HOH A:6569
BINDING SITE FOR RESIDUE HEA A 2001
16
DC1
SOFTWARE
TRP A:172 , TRP A:280 , VAL A:287 , TYR A:288 , HIS A:333 , HIS A:334 , THR A:352 , ILE A:355 , THR A:359 , GLY A:360 , ILE A:363 , GLY A:395 , GLY A:398 , ILE A:399 , LEU A:401 , SER A:402 , ASP A:407 , HIS A:411 , VAL A:416 , HIS A:419 , PHE A:420 , VAL A:423 , MET A:424 , ARG A:481 , OH A:6501 , HOH A:6506 , HOH A:6515 , HOH A:6524 , HOH A:6533 , HOH A:6553
BINDING SITE FOR RESIDUE HEA A 2002
17
DC4
SOFTWARE
MET A:56 , HOH A:6585
BINDING SITE FOR RESIDUE TRD A 5005
18
DC5
SOFTWARE
TRP A:81
BINDING SITE FOR RESIDUE TRD A 5006
19
DC6
SOFTWARE
ARG A:476 , THR B:41
BINDING SITE FOR RESIDUE TRD A 5007
20
DC7
SOFTWARE
MET A:350 , VAL A:354 , GLY B:116
BINDING SITE FOR RESIDUE TRD B 5008
21
DC8
SOFTWARE
HIS B:84
BINDING SITE FOR RESIDUE TRD A 5010
[
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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
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2gsmb1 (B:130-285)
1b: SCOP_d2gsmd1 (D:130-285)
2a: SCOP_d2gsma_ (A:)
2b: SCOP_d2gsmc_ (C:)
3a: SCOP_d2gsmb2 (B:30-129)
3b: SCOP_d2gsmd2 (D:30-129)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2gsmb1
B:130-285
1b
d2gsmd1
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
d2gsma_
A:
2b
d2gsmc_
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
d2gsmb2
B:30-129
3b
d2gsmd2
D:30-129
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2gsmB01 (B:35-130)
1b: CATH_2gsmD01 (D:35-130)
2a: CATH_2gsmC00 (C:17-550)
2b: CATH_2gsmA00 (A:17-551)
3a: CATH_2gsmB02 (B:131-283)
3b: CATH_2gsmD02 (D:131-283)
View:
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Classes
(
)
(
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Architectures
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(
)
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)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
1a
2gsmB01
B:35-130
1b
2gsmD01
D:35-130
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
2a
2gsmC00
C:17-550
2b
2gsmA00
A:17-551
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(3)
3a
2gsmB02
B:131-283
3b
2gsmD02
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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