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3FYI
Biol. Unit 1
Info
Asym.Unit (288 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (140 KB)
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(1)
Title
:
CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES IN THE REDUCED STATE BOUND WITH CYANIDE
Authors
:
L. Qin, D. A. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller
Date
:
22 Jan 09 (Deposition) - 16 Jun 09 (Release) - 16 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Conformational Changes, Cyanide Binding, Cell Membrane, Copper, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Qin, J. Liu, D. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller
Redox Dependent Conformational Changes In Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake.
Biochemistry V. 48 5121 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 19)
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: CYANIDE ION (CYNa)
4b: CYANIDE ION (CYNb)
5a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
5b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
5c: DECYL-BETA-D-MALTOPYRANOSIDE (DMUc)
5d: DECYL-BETA-D-MALTOPYRANOSIDE (DMUd)
5e: DECYL-BETA-D-MALTOPYRANOSIDE (DMUe)
5f: DECYL-BETA-D-MALTOPYRANOSIDE (DMUf)
5g: DECYL-BETA-D-MALTOPYRANOSIDE (DMUg)
5h: DECYL-BETA-D-MALTOPYRANOSIDE (DMUh)
5i: DECYL-BETA-D-MALTOPYRANOSIDE (DMUi)
5j: DECYL-BETA-D-MALTOPYRANOSIDE (DMUj)
6a: HEME-A (HEAa)
6b: HEME-A (HEAb)
6c: HEME-A (HEAc)
6d: HEME-A (HEAd)
7a: HEPTANE-1,2,3-TRIOL (HTOa)
8a: MAGNESIUM ION (MGa)
8b: MAGNESIUM ION (MGb)
9a: TRIDECANE (TRDa)
9b: TRIDECANE (TRDb)
9c: TRIDECANE (TRDc)
9d: TRIDECANE (TRDd)
9e: TRIDECANE (TRDe)
9f: TRIDECANE (TRDf)
9g: TRIDECANE (TRDg)
9h: TRIDECANE (TRDh)
9i: TRIDECANE (TRDi)
9j: TRIDECANE (TRDj)
9k: TRIDECANE (TRDk)
9l: TRIDECANE (TRDl)
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
CYN
1
Ligand/Ion
CYANIDE ION
5
DMU
6
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
6
HEA
2
Ligand/Ion
HEME-A
7
HTO
1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
8
MG
-1
Ligand/Ion
MAGNESIUM ION
9
TRD
6
Ligand/Ion
TRIDECANE
[
close Hetero Component info
]
Sites
(22, 22)
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: CC4 (SOFTWARE)
22: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
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 , GLY A:171 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , SER A:425 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , HOH A:583 , HOH A:584 , HOH A:650
BINDING SITE FOR RESIDUE HEA A 567
02
AC2
SOFTWARE
TRP A:172 , VAL A:287 , VAL A:291 , HIS A:333 , HIS A:334 , THR A:352 , ALA A:356 , GLY A:360 , PHE A:364 , PHE A:391 , GLY A:395 , VAL A:396 , 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 , CYN A:572 , HOH A:595 , HOH A:605 , HOH A:634 , HOH A:656 , HOH A:661 , PRO B:108
BINDING SITE FOR RESIDUE HEA A 568
03
AC3
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , CYN A:572
BINDING SITE FOR RESIDUE CU1 A 569
04
AC4
SOFTWARE
HIS A:411 , ASP A:412 , GLU B:254 , HOH B:318 , HOH B:327 , HOH B:334
BINDING SITE FOR RESIDUE MG A 570
05
AC5
SOFTWARE
GLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:628 , HOH A:639
BINDING SITE FOR RESIDUE CA A 571
06
AC6
SOFTWARE
HIS A:284 , HIS A:333 , HIS A:334 , HEA A:568 , CU1 A:569
BINDING SITE FOR RESIDUE CYN A 572
07
AC7
SOFTWARE
TRP A:451 , TYR A:517 , DMU A:574 , GLN B:142 , TRP B:143 , PRO B:164 , HOH B:289 , HOH B:303 , HOH B:308 , HOH B:316
BINDING SITE FOR RESIDUE DMU A 573
08
AC8
SOFTWARE
TRP A:451 , ALA A:506 , DMU A:573 , TRD A:582 , HOH A:681
BINDING SITE FOR RESIDUE DMU A 574
09
AC9
SOFTWARE
TRP A:20 , VAL A:31 , MET A:443 , SER A:444
BINDING SITE FOR RESIDUE DMU A 575
10
BC1
SOFTWARE
MET A:56 , ALA A:57 , GLN A:61 , SER A:83 , ALA A:84 , VAL A:85 , PHE A:505 , TRD A:577 , HOH A:639 , HOH A:687
BINDING SITE FOR RESIDUE DMU A 576
11
BC2
SOFTWARE
LEU A:80 , TRP A:81 , DMU A:576
BINDING SITE FOR RESIDUE TRD A 577
12
BC3
SOFTWARE
ARG A:476 , THR B:41
BINDING SITE FOR RESIDUE TRD A 578
13
BC4
SOFTWARE
MET A:350
BINDING SITE FOR RESIDUE TRD A 579
14
BC5
SOFTWARE
DMU A:574
BINDING SITE FOR RESIDUE TRD A 582
15
BC6
SOFTWARE
GLU B:152 , ALA B:276 , GLU B:280 , HOH B:291 , ALA D:276 , GLU D:280 , HIS D:283 , HOH D:1327 , HOH D:1328
BINDING SITE FOR RESIDUE HTO B 1
16
BC7
SOFTWARE
CU1 B:4 , CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260
BINDING SITE FOR RESIDUE CU1 B 3
17
BC8
SOFTWARE
CU1 B:3 , HIS B:217 , CYS B:252 , CYS B:256 , MET B:263
BINDING SITE FOR RESIDUE CU1 B 4
18
BC9
SOFTWARE
GLU B:280 , HIS B:283 , HIS B:285 , GLU D:152
BINDING SITE FOR RESIDUE CD B 8
19
CC1
SOFTWARE
HIS B:96 , GLU B:101 , HOH B:386
BINDING SITE FOR RESIDUE CD B 9
20
CC2
SOFTWARE
PHE A:364 , TRP A:371 , LEU B:75 , PHE B:94 , HIS B:96 , ASN B:97 , LEU B:100 , TRP B:104 , GLU C:86 , SER D:173 , PRO D:174 , GLU D:177 , HOH D:1151
BINDING SITE FOR RESIDUE DMU B 288
21
CC4
SOFTWARE
LEU B:120 , PRO B:121 , PHE B:124 , GLU B:128
BINDING SITE FOR RESIDUE DMU B 11
22
DC8
SOFTWARE
GLU B:152 , GLU D:280 , HIS D:283 , HIS D:285
BINDING SITE FOR RESIDUE CD D 8
[
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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:20-551)
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:20-551
-
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
-
[
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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_d3fyib2 (B:130-285)
1b: SCOP_d3fyid2 (D:130-285)
2a: SCOP_d3fyia_ (A:)
2b: SCOP_d3fyic_ (C:)
3a: SCOP_d3fyib1 (B:30-129)
3b: SCOP_d3fyid1 (D:30-129)
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Classes
(
)
(
)
Folds
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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
:
Cytochrome c oxidase
(62)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
1a
d3fyib2
B:130-285
1b
d3fyid2
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
:
Bacterial aa3 type cytochrome c oxidase subunit I
(8)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
2a
d3fyia_
A:
2b
d3fyic_
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
:
Bacterial aa3 type cytochrome c oxidase subunit II
(10)
Rhodobacter sphaeroides [TaxId: 1063]
(6)
3a
d3fyib1
B:30-129
3b
d3fyid1
D:30-129
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3fyiB01 (B:35-130)
1b: CATH_3fyiD01 (D:35-130)
2a: CATH_3fyiC00 (C:20-550)
2b: CATH_3fyiA00 (A:17-551)
3a: CATH_3fyiB02 (B:131-283)
3b: CATH_3fyiD02 (D:131-283)
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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=1.10.287.90, no name defined]
(33)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
1a
3fyiB01
B:35-130
1b
3fyiD01
D:35-130
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome C Oxidase; Chain A
(41)
Homologous Superfamily
:
Cytochrome C Oxidase, chain A
(41)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
2a
3fyiC00
C:20-550
2b
3fyiA00
A:17-551
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Rhodopseudomonas sphaeroides (Rhodobacter sphaeroides)
(3)
3a
3fyiB02
B:131-283
3b
3fyiD02
D:131-283
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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