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3OM3
Asym. Unit
Info
Asym.Unit (279 KB)
Biol.Unit 1 (139 KB)
Biol.Unit 2 (134 KB)
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(1)
Title
:
CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES WITH K362M MUTATION IN THE REDUCED STATE
Authors
:
J. Liu, L. Qin, S. Ferguson-Miller
Date
:
26 Aug 10 (Deposition) - 02 Feb 11 (Release) - 02 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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
(8, 39)
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 (I) ION (CU1a)
3b: COPPER (I) ION (CU1b)
3c: COPPER (I) ION (CU1c)
3d: COPPER (I) ION (CU1d)
3e: COPPER (I) ION (CU1e)
3f: COPPER (I) ION (CU1f)
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)
4k: DECYL-BETA-D-MALTOPYRANOSIDE (DMUk)
5a: HEME-A (HEAa)
5b: HEME-A (HEAb)
5c: HEME-A (HEAc)
5d: HEME-A (HEAd)
6a: (2S,3R)-HEPTANE-1,2,3-TRIOL (HTHa)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
CD
4
Ligand/Ion
CADMIUM ION
3
CU1
6
Ligand/Ion
COPPER (I) ION
4
DMU
11
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
HEA
4
Ligand/Ion
HEME-A
6
HTH
1
Ligand/Ion
(2S,3R)-HEPTANE-1,2,3-TRIOL
7
MG
2
Ligand/Ion
MAGNESIUM ION
8
TRD
9
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(36, 36)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:56 , GLN A:61 , PHE A:62 , PHE A:502 , TRD A:552 , HOH A:619
BINDING SITE FOR RESIDUE DMU A 1005
02
AC2
SOFTWARE
LEU A:34 , MET A:443 , SER A:444 , HOH A:561
BINDING SITE FOR RESIDUE DMU A 7
03
AC3
SOFTWARE
TYR A:50 , SER A:79
BINDING SITE FOR RESIDUE TRD A 1013
04
AC4
SOFTWARE
LEU A:34 , 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 , SER A:425 , VAL A:429 , ILE A:432 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , HOH A:587 , HOH A:589 , HOH A:626
BINDING SITE FOR RESIDUE HEA A 1
05
AC5
SOFTWARE
HOH A:15 , TRP A:172 , VAL A:287 , VAL A:291 , HIS A:333 , HIS A:334 , THR A:352 , ALA A:356 , GLY A:360 , GLY A:395 , VAL A:396 , GLY A:398 , 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 , HOH A:559 , HOH A:596
BINDING SITE FOR RESIDUE HEA A 2
06
AC6
SOFTWARE
TRP A:81 , DMU A:1005
BINDING SITE FOR RESIDUE TRD A 552
07
AC7
SOFTWARE
PHE A:469 , ARG A:476 , THR B:41
BINDING SITE FOR RESIDUE TRD A 3
08
AC8
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334
BINDING SITE FOR RESIDUE CU1 A 5
09
AC9
SOFTWARE
HIS A:411 , ASP A:412 , GLU B:254 , HOH B:503 , HOH B:766 , HOH B:769
BINDING SITE FOR RESIDUE MG A 6
10
BC1
SOFTWARE
GLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:613 , HOH A:619
BINDING SITE FOR RESIDUE CA A 553
11
BC2
SOFTWARE
TRP A:451 , PHE A:510 , GLY A:513 , HOH A:586 , DMU B:2 , HOH B:26 , GLN B:142 , TRP B:143 , PRO B:164 , HOH B:403 , HOH B:712 , HOH B:759
BINDING SITE FOR RESIDUE DMU B 1
12
BC3
SOFTWARE
TRP A:451 , HOH A:584 , DMU B:1
BINDING SITE FOR RESIDUE DMU B 2
13
BC4
SOFTWARE
TRP A:371 , PHE B:71 , LEU B:75 , HIS B:96 , ASN B:97 , TRP B:104 , GLU C:86 , SER D:173 , PRO D:174 , GLU D:177
BINDING SITE FOR RESIDUE DMU B 3
14
BC5
SOFTWARE
PRO B:121 , GLU B:128 , HOH B:493
BINDING SITE FOR RESIDUE DMU B 6
15
BC6
SOFTWARE
MET A:353 , ALA B:117
BINDING SITE FOR RESIDUE TRD B 4
16
BC7
SOFTWARE
GLU B:152 , ALA B:276 , GLU B:280 , HIS B:283 , HOH B:709 , ALA D:276 , GLU D:280 , HIS D:283
BINDING SITE FOR RESIDUE HTH B 286
17
BC8
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260 , CU1 B:288
BINDING SITE FOR RESIDUE CU1 B 287
18
BC9
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263 , CU1 B:287
BINDING SITE FOR RESIDUE CU1 B 288
19
CC1
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 8
20
CC2
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:708 , HOH B:741 , HOH B:742
BINDING SITE FOR RESIDUE CD B 9
21
CC3
SOFTWARE
MET C:56 , GLN C:61 , PHE C:62 , SER C:83 , ALA C:84 , VAL C:85 , PHE C:502 , TRD C:552 , HOH C:573
BINDING SITE FOR RESIDUE DMU C 10
22
CC4
SOFTWARE
TRP C:451
BINDING SITE FOR RESIDUE DMU C 5
23
CC5
SOFTWARE
MET C:443
BINDING SITE FOR RESIDUE DMU C 9
24
CC6
SOFTWARE
LEU C:34 , GLY C:38 , VAL C:45 , 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:555 , HOH C:575
BINDING SITE FOR RESIDUE HEA C 1
25
CC7
SOFTWARE
HOH C:15 , TRP C:172 , TRP C:280 , VAL C:287 , VAL C:291 , HIS C:333 , HIS C:334 , GLY C:360 , PHE C:391 , GLY C:395 , VAL C:396 , GLY C:398 , ILE C:399 , 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:577 , PRO D:108
BINDING SITE FOR RESIDUE HEA C 2
26
CC8
SOFTWARE
DMU C:10 , TRP C:81 , PRO C:82
BINDING SITE FOR RESIDUE TRD C 552
27
CC9
SOFTWARE
ARG C:476 , THR D:41
BINDING SITE FOR RESIDUE TRD C 3
28
DC1
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334
BINDING SITE FOR RESIDUE CU1 C 553
29
DC2
SOFTWARE
HIS C:411 , ASP C:412 , HOH C:564 , HOH C:568 , GLU D:254 , HOH D:304
BINDING SITE FOR RESIDUE MG C 6
30
DC3
SOFTWARE
GLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:565 , HOH C:573
BINDING SITE FOR RESIDUE CA C 7
31
DC4
SOFTWARE
LEU D:120 , PRO D:121 , ASN D:125 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 4
32
DC5
SOFTWARE
HIS D:96 , ASN D:97
BINDING SITE FOR RESIDUE DMU D 8
33
DC6
SOFTWARE
CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260 , CU1 D:286
BINDING SITE FOR RESIDUE CU1 D 3
34
DC7
SOFTWARE
CU1 D:3 , HIS D:217 , CYS D:252 , CYS D:256 , MET D:263
BINDING SITE FOR RESIDUE CU1 D 286
35
DC8
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 287
36
DC9
SOFTWARE
HIS D:96 , GLU D:101
BINDING SITE FOR RESIDUE CD D 9
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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Label:
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_d3om3b2 (B:130-285)
1b: SCOP_d3om3d2 (D:130-285)
2a: SCOP_d3om3a_ (A:)
2b: SCOP_d3om3c_ (C:)
3a: SCOP_d3om3b1 (B:30-129)
3b: SCOP_d3om3d1 (D:30-129)
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Classes
(
)
(
)
Folds
(
)
(
)
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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
d3om3b2
B:130-285
1b
d3om3d2
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
d3om3a_
A:
2b
d3om3c_
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
d3om3b1
B:30-129
3b
d3om3d1
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_3om3D01 (D:134-270)
1b: PFAM_COX2_3om3D02 (D:134-270)
2a: PFAM_COX1_3om3C01 (C:26-504)
2b: PFAM_COX1_3om3C02 (C:26-504)
3a: PFAM_COX2_TM_3om3D03 (D:35-122)
3b: PFAM_COX2_TM_3om3D04 (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
COX2-3om3D01
D:134-270
1b
COX2-3om3D02
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
COX1-3om3C01
C:26-504
2b
COX1-3om3C02
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-3om3D03
D:35-122
3b
COX2_TM-3om3D04
D:35-122
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