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3OM3
Biol. Unit 2
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:
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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, 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 (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
-1
Ligand/Ion
CALCIUM ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
CU1
3
Ligand/Ion
COPPER (I) ION
4
DMU
5
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
HEA
2
Ligand/Ion
HEME-A
6
HTH
-1
Ligand/Ion
(2S,3R)-HEPTANE-1,2,3-TRIOL
7
MG
-1
Ligand/Ion
MAGNESIUM ION
8
TRD
3
Ligand/Ion
TRIDECANE
[
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Sites
(19, 19)
Info
All Sites
01: BC4 (SOFTWARE)
02: BC7 (SOFTWARE)
03: CC1 (SOFTWARE)
04: CC3 (SOFTWARE)
05: CC4 (SOFTWARE)
06: CC5 (SOFTWARE)
07: CC6 (SOFTWARE)
08: CC7 (SOFTWARE)
09: CC8 (SOFTWARE)
10: CC9 (SOFTWARE)
11: DC1 (SOFTWARE)
12: DC2 (SOFTWARE)
13: DC3 (SOFTWARE)
14: DC4 (SOFTWARE)
15: DC5 (SOFTWARE)
16: DC6 (SOFTWARE)
17: DC7 (SOFTWARE)
18: DC8 (SOFTWARE)
19: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
CC1
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 8
04
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
05
CC4
SOFTWARE
TRP C:451
BINDING SITE FOR RESIDUE DMU C 5
06
CC5
SOFTWARE
MET C:443
BINDING SITE FOR RESIDUE DMU C 9
07
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
08
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
09
CC8
SOFTWARE
DMU C:10 , TRP C:81 , PRO C:82
BINDING SITE FOR RESIDUE TRD C 552
10
CC9
SOFTWARE
ARG C:476 , THR D:41
BINDING SITE FOR RESIDUE TRD C 3
11
DC1
SOFTWARE
HIS C:284 , HIS C:333 , HIS C:334
BINDING SITE FOR RESIDUE CU1 C 553
12
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
13
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
14
DC4
SOFTWARE
LEU D:120 , PRO D:121 , ASN D:125 , GLU D:128
BINDING SITE FOR RESIDUE DMU D 4
15
DC5
SOFTWARE
HIS D:96 , ASN D:97
BINDING SITE FOR RESIDUE DMU D 8
16
DC6
SOFTWARE
CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260 , CU1 D:286
BINDING SITE FOR RESIDUE CU1 D 3
17
DC7
SOFTWARE
CU1 D:3 , HIS D:217 , CYS D:252 , CYS D:256 , MET D:263
BINDING SITE FOR RESIDUE CU1 D 286
18
DC8
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 287
19
DC9
SOFTWARE
HIS D:96 , GLU D:101
BINDING SITE FOR RESIDUE CD D 9
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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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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_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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(
)
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
:
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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Families
(
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(
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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
COX2-3om3D01
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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Asymmetric Unit 1
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