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3OMI
Asym. Unit
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
[
close entry info
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Hetero Components
(11, 43)
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)
03a: CHLORIDE ION (CLa)
03b: CHLORIDE ION (CLb)
04a: COPPER (I) ION (CU1a)
04b: COPPER (I) ION (CU1b)
05a: COPPER (II) ION (CUa)
05b: COPPER (II) ION (CUb)
05c: COPPER (II) ION (CUc)
05d: COPPER (II) ION (CUd)
06a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
06b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
06c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
06d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
06e: DECYL-BETA-D-MALTOPYRANOSIDE (DMUe)
06f: DECYL-BETA-D-MALTOPYRANOSIDE (DMUf)
06g: DECYL-BETA-D-MALTOPYRANOSIDE (DMUg)
06h: DECYL-BETA-D-MALTOPYRANOSIDE (DMUh)
06i: DECYL-BETA-D-MALTOPYRANOSIDE (DMUi)
06j: DECYL-BETA-D-MALTOPYRANOSIDE (DMUj)
06k: DECYL-BETA-D-MALTOPYRANOSIDE (DMUk)
07a: HEME-A (HEAa)
07b: HEME-A (HEAb)
07c: HEME-A (HEAc)
07d: HEME-A (HEAd)
08a: (2S,3R)-HEPTANE-1,2,3-TRIOL (HTHa)
09a: MAGNESIUM ION (MGa)
09b: 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
2
Ligand/Ion
CALCIUM ION
2
CD
4
Ligand/Ion
CADMIUM ION
3
CL
2
Ligand/Ion
CHLORIDE ION
5
CU
4
Ligand/Ion
COPPER (II) ION
4
CU1
2
Ligand/Ion
COPPER (I) ION
6
DMU
11
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
7
HEA
4
Ligand/Ion
HEME-A
8
HTH
1
Ligand/Ion
(2S,3R)-HEPTANE-1,2,3-TRIOL
9
MG
2
Ligand/Ion
MAGNESIUM ION
10
OH
2
Ligand/Ion
HYDROXIDE ION
11
TRD
9
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(39, 39)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:284 , VAL A:287 , HIS A:334 , HEA A:608 , CU A:611 , HOH A:744
BINDING SITE FOR RESIDUE OH A 601
02
AC2
SOFTWARE
TRP A:20 , VAL A:31 , LEU A:34 , MET A:443 , SER A:444 , HOH A:730
BINDING SITE FOR RESIDUE DMU A 602
03
AC3
SOFTWARE
MET A:56 , ALA A:57 , GLN A:61 , PHE A:502 , TRD A:609 , HOH A:817
BINDING SITE FOR RESIDUE DMU A 603
04
AC4
SOFTWARE
PHE A:76 , SER A:79
BINDING SITE FOR RESIDUE TRD A 605
05
AC5
SOFTWARE
LEU A:34 , GLY A:38 , VAL A:45 , THR A:48 , MET A:51 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , MET A:106 , MET A:107 , VAL A:111 , GLY A:171 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , MET A:424 , SER A:425 , VAL A:429 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , PHE A:508 , HOH A:784 , HOH A:786 , HOH A:827
BINDING SITE FOR RESIDUE HEA A 607
06
AC6
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 , 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:601 , HOH A:708 , HOH A:718 , HOH A:727 , HOH A:744 , HOH A:794 , ILE B:68
BINDING SITE FOR RESIDUE HEA A 608
07
AC7
SOFTWARE
LEU A:80 , TRP A:81 , DMU A:603
BINDING SITE FOR RESIDUE TRD A 609
08
AC8
SOFTWARE
ARG A:476 , THR B:41
BINDING SITE FOR RESIDUE TRD A 610
09
AC9
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , OH A:601 , HOH A:744
BINDING SITE FOR RESIDUE CU A 611
10
BC1
SOFTWARE
HIS A:411 , ASP A:412 , GLU B:254 , HOH B:428 , HOH B:514 , HOH B:518
BINDING SITE FOR RESIDUE MG A 612
11
BC2
SOFTWARE
GLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:810 , HOH A:817
BINDING SITE FOR RESIDUE CA A 613
12
BC3
SOFTWARE
HIS A:26 , MET A:133 , HOH A:828 , HOH A:832
BINDING SITE FOR RESIDUE CL A 614
13
BC4
SOFTWARE
PRO A:449 , TRP A:451 , PHE A:510 , GLY A:513 , GLN B:142 , TRP B:143 , PRO B:164 , DMU B:302 , HOH B:407 , HOH B:409 , HOH B:435 , HOH B:506
BINDING SITE FOR RESIDUE DMU B 301
14
BC5
SOFTWARE
TRP A:451 , ALA A:506 , HOH A:780 , DMU B:301
BINDING SITE FOR RESIDUE DMU B 302
15
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
16
BC7
SOFTWARE
PRO B:121 , PHE B:124 , GLU B:128
BINDING SITE FOR RESIDUE DMU B 304
17
BC8
SOFTWARE
LEU B:112 , VAL B:113 , GLY B:116 , ALA B:117
BINDING SITE FOR RESIDUE TRD B 305
18
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
19
CC1
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260 , CU1 B:308
BINDING SITE FOR RESIDUE CU B 307
20
CC2
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263 , CU B:307
BINDING SITE FOR RESIDUE CU1 B 308
21
CC3
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 309
22
CC4
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:430 , HOH B:482 , HOH B:483
BINDING SITE FOR RESIDUE CD B 310
23
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
24
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
25
CC7
SOFTWARE
MET C:443 , SER C:444
BINDING SITE FOR RESIDUE DMU C 604
26
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
27
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
28
DC1
SOFTWARE
LEU C:80 , TRP C:81 , PRO C:82 , DMU C:602
BINDING SITE FOR RESIDUE TRD C 607
29
DC2
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334 , OH C:601 , HOH C:795
BINDING SITE FOR RESIDUE CU C 608
30
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
31
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
32
DC5
SOFTWARE
HIS C:26 , ALA C:132 , MET C:133
BINDING SITE FOR RESIDUE CL C 611
33
DC6
SOFTWARE
PRO D:121 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 301
34
DC7
SOFTWARE
HIS D:96 , ASN D:97
BINDING SITE FOR RESIDUE DMU D 302
35
DC8
SOFTWARE
ARG C:476 , THR D:41
BINDING SITE FOR RESIDUE TRD D 303
36
DC9
SOFTWARE
CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260 , CU1 D:306
BINDING SITE FOR RESIDUE CU D 305
37
EC1
SOFTWARE
HIS D:217 , CYS D:252 , CYS D:256 , MET D:263 , CU D:305
BINDING SITE FOR RESIDUE CU1 D 306
38
EC2
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 307
39
EC3
SOFTWARE
HIS D:96 , GLU D:101 , HOH D:501 , HOH D:502
BINDING SITE FOR RESIDUE CD D 308
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 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
View:
Label:
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_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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(
)
(
)
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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
:
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
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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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