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3OMI
Biol. Unit 2
Info
Asym.Unit (285 KB)
Biol.Unit 1 (141 KB)
Biol.Unit 2 (138 KB)
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(1)
Title
:
CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES WITH D132A MUTATION
Authors
:
J. Liu, L. Qin, S. Ferguson-Miller
Date
:
27 Aug 10 (Deposition) - 02 Feb 11 (Release) - 19 Nov 14 (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, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Liu, L. Qin, S. Ferguson-Miller
Crystallographic And Online Spectral Evidence For Role Of Conformational Change And Conserved Water In Cytochrome Oxidase Proton Pump.
Proc. Natl. Acad. Sci. Usa V. 108 1284 2011
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Hetero Components
(4, 11)
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: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: COPPER (I) ION (CU1a)
4b: COPPER (I) ION (CU1b)
5a: COPPER (II) ION (CUa)
5b: COPPER (II) ION (CUb)
5c: COPPER (II) ION (CUc)
5d: COPPER (II) ION (CUd)
6a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
6b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
6c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
6d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
6e: DECYL-BETA-D-MALTOPYRANOSIDE (DMUe)
6f: DECYL-BETA-D-MALTOPYRANOSIDE (DMUf)
6g: DECYL-BETA-D-MALTOPYRANOSIDE (DMUg)
6h: DECYL-BETA-D-MALTOPYRANOSIDE (DMUh)
6i: DECYL-BETA-D-MALTOPYRANOSIDE (DMUi)
6j: DECYL-BETA-D-MALTOPYRANOSIDE (DMUj)
6k: DECYL-BETA-D-MALTOPYRANOSIDE (DMUk)
7a: HEME-A (HEAa)
7b: HEME-A (HEAb)
7c: HEME-A (HEAc)
7d: HEME-A (HEAd)
8a: (2S,3R)-HEPTANE-1,2,3-TRIOL (HTHa)
9a: MAGNESIUM ION (MGa)
9b: MAGNESIUM ION (MGb)
10a: HYDROXIDE ION (OHa)
10b: HYDROXIDE ION (OHb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
5
CU
-1
Ligand/Ion
COPPER (II) ION
4
CU1
1
Ligand/Ion
COPPER (I) ION
6
DMU
5
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
7
HEA
2
Ligand/Ion
HEME-A
8
HTH
-1
Ligand/Ion
(2S,3R)-HEPTANE-1,2,3-TRIOL
9
MG
-1
Ligand/Ion
MAGNESIUM ION
10
OH
-1
Ligand/Ion
HYDROXIDE ION
11
TRD
3
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: BC6 (SOFTWARE)
02: BC9 (SOFTWARE)
03: CC3 (SOFTWARE)
04: CC5 (SOFTWARE)
05: CC6 (SOFTWARE)
06: CC7 (SOFTWARE)
07: CC8 (SOFTWARE)
08: CC9 (SOFTWARE)
09: DC1 (SOFTWARE)
10: DC2 (SOFTWARE)
11: DC3 (SOFTWARE)
12: DC4 (SOFTWARE)
13: DC5 (SOFTWARE)
14: DC6 (SOFTWARE)
15: DC7 (SOFTWARE)
16: DC8 (SOFTWARE)
17: DC9 (SOFTWARE)
18: EC1 (SOFTWARE)
19: EC2 (SOFTWARE)
20: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC6
SOFTWARE
TRP A:371 , PHE B:94 , HIS B:96 , ASN B:97 , LEU B:100 , TRP B:104 , HOH B:422 , GLU C:86 , SER D:173 , PRO D:174 , GLU D:177 , HOH D:483
BINDING SITE FOR RESIDUE DMU B 303
02
BC9
SOFTWARE
GLU B:152 , ALA B:276 , GLU B:280 , HIS B:283 , HOH B:431 , ALA D:276 , GLU D:280 , HIS D:283
BINDING SITE FOR RESIDUE HTH B 306
03
CC3
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 309
04
CC5
SOFTWARE
HIS C:284 , VAL C:287 , HIS C:334 , HEA C:606 , CU C:608 , HOH C:795
BINDING SITE FOR RESIDUE OH C 601
05
CC6
SOFTWARE
MET C:53 , MET C:56 , GLN C:61 , SER C:83 , PHE C:502 , PHE C:505 , TRD C:607 , HOH C:735
BINDING SITE FOR RESIDUE DMU C 602
06
CC7
SOFTWARE
MET C:443 , SER C:444
BINDING SITE FOR RESIDUE DMU C 604
07
CC8
SOFTWARE
LEU C:34 , GLY C:38 , 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 , MET C:460 , PHE C:468 , GLN C:471 , ARG C:481 , ARG C:482 , SER C:504 , HOH C:701 , HOH C:736 , HOH C:766
BINDING SITE FOR RESIDUE HEA C 605
08
CC9
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 , OH C:601 , HOH C:708 , HOH C:739 , HOH C:744 , HOH C:757 , HOH C:795
BINDING SITE FOR RESIDUE HEA C 606
09
DC1
SOFTWARE
LEU C:80 , TRP C:81 , PRO C:82 , DMU C:602
BINDING SITE FOR RESIDUE TRD C 607
10
DC2
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334 , OH C:601 , HOH C:795
BINDING SITE FOR RESIDUE CU C 608
11
DC3
SOFTWARE
HIS C:411 , ASP C:412 , HOH C:721 , GLU D:254 , HOH D:436 , HOH D:438
BINDING SITE FOR RESIDUE MG C 609
12
DC4
SOFTWARE
GLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:722 , HOH C:735
BINDING SITE FOR RESIDUE CA C 610
13
DC5
SOFTWARE
HIS C:26 , ALA C:132 , MET C:133
BINDING SITE FOR RESIDUE CL C 611
14
DC6
SOFTWARE
PRO D:121 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 301
15
DC7
SOFTWARE
HIS D:96 , ASN D:97
BINDING SITE FOR RESIDUE DMU D 302
16
DC8
SOFTWARE
ARG C:476 , THR D:41
BINDING SITE FOR RESIDUE TRD D 303
17
DC9
SOFTWARE
CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260 , CU1 D:306
BINDING SITE FOR RESIDUE CU D 305
18
EC1
SOFTWARE
HIS D:217 , CYS D:252 , CYS D:256 , MET D:263 , CU D:305
BINDING SITE FOR RESIDUE CU1 D 306
19
EC2
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 307
20
EC3
SOFTWARE
HIS D:96 , GLU D:101 , HOH D:501 , HOH D:502
BINDING SITE FOR RESIDUE CD D 308
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
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End label:
Sorry, no Info available
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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_d3omib2 (B:130-285)
1b: SCOP_d3omid2 (D:130-285)
2a: SCOP_d3omia_ (A:)
2b: SCOP_d3omic_ (C:)
3a: SCOP_d3omib1 (B:30-129)
3b: SCOP_d3omid1 (D:30-129)
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Classes
(
)
(
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(
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(
)
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(
)
(
)
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
:
automated matches
(5)
Rhodobacter sphaeroides [TaxId: 272943]
(4)
1a
d3omib2
B:130-285
1b
d3omid2
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
:
automated matches
(24)
Rhodobacter sphaeroides [TaxId: 272943]
(4)
2a
d3omia_
A:
2b
d3omic_
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
:
automated matches
(4)
Rhodobacter sphaeroides [TaxId: 272943]
(4)
3a
d3omib1
B:30-129
3b
d3omid1
D:30-129
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_COX2_3omiD01 (D:134-270)
1b: PFAM_COX2_3omiD02 (D:134-270)
2a: PFAM_COX1_3omiC01 (C:26-504)
2b: PFAM_COX1_3omiC02 (C:26-504)
3a: PFAM_COX2_TM_3omiD03 (D:35-122)
3b: PFAM_COX2_TM_3omiD04 (D:35-122)
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Clans
(
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(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
COX2
(19)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
(4)
1a
COX2-3omiD01
D:134-270
1b
COX2-3omiD02
D:134-270
Clan
:
no clan defined [family: COX1]
(19)
Family
:
COX1
(19)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
(4)
2a
COX1-3omiC01
C:26-504
2b
COX1-3omiC02
C:26-504
Clan
:
no clan defined [family: COX2_TM]
(16)
Family
:
COX2_TM
(16)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
(4)
3a
COX2_TM-3omiD03
D:35-122
3b
COX2_TM-3omiD04
D:35-122
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Asymmetric Unit 1
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