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1M56
Biol. Unit 1
Info
Asym.Unit (398 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (195 KB)
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(1)
Title
:
STRUCTURE OF CYTOCHROME C OXIDASE FROM RHODOBACTOR SPHAEROIDES (WILD TYPE)
Authors
:
M. Svensson-Ek, J. Abramson, G. Larsson, S. Tornroth, P. Brezezinski, S. Iwata
Date
:
08 Jul 02 (Deposition) - 28 Aug 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,G,H,I,J
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: G,H,I,J (1x)
Keywords
:
Membrane Protein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Svensson-Ek, J. Abramson, G. Larsson, S. Tornroth, P. Brzezinski, S. Iwata
The X-Ray Crystal Structures Of Wild-Type And Eq(I-286) Mutant Cytochrome C Oxidases From Rhodobacter Sphaeroides.
J. Mol. Biol. V. 321 329 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
2e: COPPER (II) ION (CUe)
2f: COPPER (II) ION (CUf)
3a: HEME-A (HEAa)
3b: HEME-A (HEAb)
3c: HEME-A (HEAc)
3d: HEME-A (HEAd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHa)
5b: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHb)
5c: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHc)
5d: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHd)
5e: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHe)
5f: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHf)
5g: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHg)
5h: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHh)
5i: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHi)
5j: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHj)
5k: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHk)
5l: DI-STEAROYL-3-SN-PHOSPHATIDYLETHAN... (PEHl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CU
-1
Ligand/Ion
COPPER (II) ION
3
HEA
2
Ligand/Ion
HEME-A
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
PEH
6
Ligand/Ion
DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260 , CU B:1004
BINDING SITE FOR RESIDUE CU B 1003
02
AC2
SOFTWARE
HIS B:217 , CYS B:252 , CYS B:256 , MET B:263 , CU B:1003
BINDING SITE FOR RESIDUE CU B 1004
03
AC3
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334
BINDING SITE FOR RESIDUE CU A 1005
04
AC4
SOFTWARE
HIS A:411 , ASP A:412 , HOH A:2060 , GLU B:254 , HOH B:1007 , HOH B:1010
BINDING SITE FOR RESIDUE MG A 2006
05
AC5
SOFTWARE
GLU A:54 , ALA A:57 , PRO A:58 , GLY A:59 , GLN A:61 , HOH A:2061
BINDING SITE FOR RESIDUE CA A 1007
06
BC2
SOFTWARE
LEU A:34 , GLY A:38 , VAL A:45 , THR A:48 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , GLY A:103 , MET A:106 , MET A:107 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , MET A:424 , SER A:425 , VAL A:429 , ILE A:432 , ILE A:436 , THR A:467 , PHE A:468 , ARG A:481 , ARG A:482 , ALA A:501 , SER A:504 , PHE A:508 , HOH A:2019 , HOH A:2057
BINDING SITE FOR RESIDUE HEA A 1001
07
BC3
SOFTWARE
TRP A:172 , TRP A:280 , VAL A:287 , TYR A:288 , HIS A:333 , HIS A:334 , ILE A:355 , THR A:359 , GLY A:360 , PHE A:391 , 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:2015 , HOH A:2023 , HOH A:2050 , ILE B:68 , PRO B:108
BINDING SITE FOR RESIDUE HEA A 1002
08
BC4
SOFTWARE
TRP C:59 , VAL C:62 , VAL C:63 , SER C:66 , HIS C:71 , PHE C:83 , PHE C:86 , PHE C:219 , ARG C:226 , HIS C:231 , PHE C:232 , VAL C:238 , GLY C:239 , HOH C:2040
BINDING SITE FOR RESIDUE PEH C 2008
09
BC5
SOFTWARE
PHE A:135 , PRO A:136 , ARG A:137 , MET A:138 , ALA A:199 , ILE A:202 , ALA A:247 , LEU C:12 , TRP C:58 , TRP C:59 , GLY C:82 , PHE C:83 , PHE C:86
BINDING SITE FOR RESIDUE PEH A 2009
10
BC6
SOFTWARE
TRP A:331 , GLN A:344 , PEH A:2012 , ARG B:234 , VAL C:91 , TRP C:99 , LYS C:103 , TYR C:107 , PHE C:249 , VAL C:252 , VAL C:253 , PHE C:256 , PEH C:2013 , ALA D:36 , PEH D:2011
BINDING SITE FOR RESIDUE PEH C 2010
11
BC7
SOFTWARE
LEU A:241 , GLN A:344 , TYR A:347 , PEH A:2012 , TYR C:107 , LEU C:255 , PHE C:256 , PEH C:2010 , ILE D:39 , LEU D:43 , ALA D:47 , ASN D:50 , ALA D:51 , HOH D:72
BINDING SITE FOR RESIDUE PEH D 2011
12
BC8
SOFTWARE
ARG A:216 , THR A:221 , MET A:222 , TRP A:230 , TRP A:237 , VAL A:325 , VAL C:91 , PEH C:2010 , LYS D:23 , THR D:24 , MET D:31 , ALA D:35 , PEH D:2011
BINDING SITE FOR RESIDUE PEH A 2012
13
BC9
SOFTWARE
ARG C:80 , ILE C:84 , HIS C:152 , TRP C:245 , PEH C:2010 , PHE D:25 , ALA D:36 , VAL D:37
BINDING SITE FOR RESIDUE PEH C 2013
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: COX1 (A:20-558)
2: COX2_TM (B:35-130)
3: COX2_CUA (B:131-281)
4: COX2 (B:215-263)
5: COX1_CUB (A: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
1
A:20-558
-
2
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_RHOSH
35-130
1
B:35-130
-
3
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_RHOSH
131-281
1
B:131-281
-
4
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_RHOSH
215-263
1
B:215-263
-
5
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_RHOSH
280-334
1
A:280-334
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1m56b1 (B:130-289)
1b: SCOP_d1m56h1 (H:130-289)
2a: SCOP_d1m56a_ (A:)
2b: SCOP_d1m56g_ (G:)
3a: SCOP_d1m56c_ (C:)
3b: SCOP_d1m56i_ (I:)
4a: SCOP_d1m56d_ (D:)
4b: SCOP_d1m56j_ (J:)
5a: SCOP_d1m56b2 (B:30-129)
5b: SCOP_d1m56h2 (H:30-129)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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
:
Cytochrome c oxidase
(62)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
1a
d1m56b1
B:130-289
1b
d1m56h1
H:130-289
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
d1m56a_
A:
2b
d1m56g_
G:
Fold
:
Cytochrome c oxidase subunit III-like
(29)
Superfamily
:
Cytochrome c oxidase subunit III-like
(29)
Family
:
Cytochrome c oxidase subunit III-like
(29)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit III
(3)
Rhodobacter sphaeroides [TaxId: 1063]
(2)
3a
d1m56c_
C:
3b
d1m56i_
I:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Bacterial aa3 type cytochrome c oxidase subunit IV
(3)
Family
:
Bacterial aa3 type cytochrome c oxidase subunit IV
(3)
Protein domain
:
Bacterial aa3 type cytochrome c oxidase subunit IV
(3)
Rhodobacter sphaeroides [TaxId: 1063]
(2)
4a
d1m56d_
D:
4b
d1m56j_
J:
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)
5a
d1m56b2
B:30-129
5b
d1m56h2
H:30-129
[
close SCOP info
]
CATH Domains
(6, 12)
Info
all CATH domains
1a: CATH_1m56C01 (C:2-70)
1b: CATH_1m56I01 (I:2-70)
2a: CATH_1m56B01 (B:35-130)
2b: CATH_1m56H01 (H:35-130)
3a: CATH_1m56A00 (A:14-560)
3b: CATH_1m56G00 (G:14-560)
4a: CATH_1m56C02 (C:71-266)
4b: CATH_1m56I02 (I:71-266)
5a: CATH_1m56D00 (D:10-51)
5b: CATH_1m56J00 (J:10-51)
6a: CATH_1m56B02 (B:131-283)
6b: CATH_1m56H02 (H:131-283)
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)
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)
Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.70, no name defined]
(106)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
1a
1m56C01
C:2-70
1b
1m56I01
I:2-70
Homologous Superfamily
:
[code=1.10.287.90, no name defined]
(33)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
2a
1m56B01
B:35-130
2b
1m56H01
H: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. Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
3a
1m56A00
A:14-560
3b
1m56G00
G:14-560
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.80, no name defined]
(26)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
4a
1m56C02
C:71-266
4b
1m56I02
I:71-266
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.160, no name defined]
(3)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
5a
1m56D00
D:10-51
5b
1m56J00
J:10-51
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063. Rhodobacter sphaeroides. Organism_taxid: 1063.
(1)
6a
1m56B02
B:131-283
6b
1m56H02
H:131-283
[
close CATH info
]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_COX2_1m56H01 (H:134-270)
1b: PFAM_COX2_1m56H02 (H:134-270)
2a: PFAM_COX1_1m56G01 (G:26-504)
2b: PFAM_COX1_1m56G02 (G:26-504)
3a: PFAM_COX2_TM_1m56H03 (H:35-122)
3b: PFAM_COX2_TM_1m56H04 (H:35-122)
4a: PFAM_COX3_1m56I01 (I:7-266)
4b: PFAM_COX3_1m56I02 (I:7-266)
5a: PFAM_COX4_pro_2_1m56J01 (J:10-51)
5b: PFAM_COX4_pro_2_1m56J02 (J:10-51)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
COX2
(19)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(2)
1a
COX2-1m56H01
H:134-270
1b
COX2-1m56H02
H:134-270
Clan
:
no clan defined [family: COX1]
(19)
Family
:
COX1
(19)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(2)
2a
COX1-1m56G01
G:26-504
2b
COX1-1m56G02
G:26-504
Clan
:
no clan defined [family: COX2_TM]
(16)
Family
:
COX2_TM
(16)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(2)
3a
COX2_TM-1m56H03
H:35-122
3b
COX2_TM-1m56H04
H:35-122
Clan
:
no clan defined [family: COX3]
(12)
Family
:
COX3
(12)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(2)
4a
COX3-1m56I01
I:7-266
4b
COX3-1m56I02
I:7-266
Clan
:
no clan defined [family: COX4_pro_2]
(3)
Family
:
COX4_pro_2
(3)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(2)
5a
COX4_pro_2-1m56J01
J:10-51
5b
COX4_pro_2-1m56J02
J:10-51
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