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2GSM
Asym. Unit
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
[
close entry info
]
Hetero Components
(8, 42)
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
2
Ligand/Ion
CALCIUM ION
2
CD
4
Ligand/Ion
CADMIUM ION
3
CU
6
Ligand/Ion
COPPER (II) ION
4
DMU
10
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
HEA
4
Ligand/Ion
HEME-A
6
MG
2
Ligand/Ion
MAGNESIUM ION
7
OH
2
Ligand/Ion
HYDROXIDE ION
8
TRD
12
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(38, 38)
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)
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
AC6
SOFTWARE
TRP C:451 , TRD C:6001
BINDING SITE FOR RESIDUE DMU C 6002
07
AC7
SOFTWARE
HIS D:96 , ASN D:97
BINDING SITE FOR RESIDUE DMU D 6003
08
AC8
SOFTWARE
TRP C:20 , MET C:443 , SER C:444 , ILE C:515 , HOH C:1102
BINDING SITE FOR RESIDUE DMU C 6004
09
AC9
SOFTWARE
GLN C:61 , PHE C:62 , PRO C:82 , HOH C:1152 , HOH C:1164
BINDING SITE FOR RESIDUE DMU C 6005
10
BC1
SOFTWARE
PRO D:121 , PHE D:124 , ASN D:125 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 6011
11
BC2
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260 , CU B:3004
BINDING SITE FOR RESIDUE CU B 3003
12
BC3
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263 , CU B:3003
BINDING SITE FOR RESIDUE CU B 3004
13
BC4
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , OH A:6501 , HOH A:6506
BINDING SITE FOR RESIDUE CU A 3005
14
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
15
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
16
BC7
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 3008
17
BC8
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:5113 , HOH B:5114
BINDING SITE FOR RESIDUE CD B 3009
18
BC9
SOFTWARE
CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260 , CU D:4004
BINDING SITE FOR RESIDUE CU D 4003
19
CC1
SOFTWARE
HIS D:217 , CYS D:252 , CYS D:256 , MET D:263 , CU D:4003
BINDING SITE FOR RESIDUE CU D 4004
20
CC2
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334 , HOH C:1006 , OH C:7501
BINDING SITE FOR RESIDUE CU C 4005
21
CC3
SOFTWARE
HIS C:411 , ASP C:412 , GLU D:254 , HOH D:1071 , HOH D:1082 , HOH D:1094
BINDING SITE FOR RESIDUE MG C 4006
22
CC4
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 4007
23
CC5
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 4008
24
CC6
SOFTWARE
HIS D:96 , GLU D:101 , HOH D:1196 , HOH D:1197
BINDING SITE FOR RESIDUE CD D 4009
25
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
26
CC8
SOFTWARE
HIS C:284 , VAL C:287 , HIS C:334 , HOH C:1006 , HEA C:3002 , CU C:4005
BINDING SITE FOR RESIDUE OH C 7501
27
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
28
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
29
DC2
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 , VAL C:111 , GLY C:171 , TRP C:172 , TYR C:414 , PHE C:420 , HIS C:421 , MET C:424 , SER C:425 , VAL C:429 , PHE C:468 , GLN C:471 , ARG C:481 , ARG C:482 , SER C:504 , PHE C:508 , HOH C:1001 , HOH C:1003 , HOH C:1130
BINDING SITE FOR RESIDUE HEA C 3001
30
DC3
SOFTWARE
TRP C:172 , TRP C:280 , VAL C:287 , TYR C:288 , HIS C:333 , HIS C:334 , THR C:352 , ILE C:355 , THR C:359 , GLY C:360 , GLY C:395 , GLY C:398 , 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:1006 , HOH C:1015 , HOH C:1030 , HOH C:1048 , HOH C:1096 , OH C:7501
BINDING SITE FOR RESIDUE HEA C 3002
31
DC4
SOFTWARE
MET A:56 , HOH A:6585
BINDING SITE FOR RESIDUE TRD A 5005
32
DC5
SOFTWARE
TRP A:81
BINDING SITE FOR RESIDUE TRD A 5006
33
DC6
SOFTWARE
ARG A:476 , THR B:41
BINDING SITE FOR RESIDUE TRD A 5007
34
DC7
SOFTWARE
MET A:350 , VAL A:354 , GLY B:116
BINDING SITE FOR RESIDUE TRD B 5008
35
DC8
SOFTWARE
HIS B:84
BINDING SITE FOR RESIDUE TRD A 5010
36
DC9
SOFTWARE
TRP C:451 , GLY C:513 , DMU C:6002
BINDING SITE FOR RESIDUE TRD C 6001
37
EC1
SOFTWARE
LEU C:80 , TRP C:81 , PRO C:82
BINDING SITE FOR RESIDUE TRD C 6006
38
EC2
SOFTWARE
ARG C:476 , THR D:41
BINDING SITE FOR RESIDUE TRD D 6007
[
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:20-550)
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:
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
2
A:20-551
C:20-550
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_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)
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Protein Domains
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(
)
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)
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Homologous Superfamilies
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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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