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2YEV
Biol. Unit 1
Info
Asym.Unit (815 KB)
Biol.Unit 1 (404 KB)
Biol.Unit 2 (403 KB)
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(1)
Title
:
STRUCTURE OF CAA3-TYPE CYTOCHROME OXIDASE
Authors
:
J. A. Lyons, D. Aragao, T. Soulimane, M. Caffrey
Date
:
31 Mar 11 (Deposition) - 23 May 12 (Release) - 29 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.36
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: D,E,F (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. Lyons, D. Aragao, O. Slattery, A. V. Pisliakov, T. Soulimane, M. Caffrey
Structural Insights Into Electron Transfer In Caa3-Type Cytochrome Oxidases.
Nature V. 487 514 2012
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: (2R)-3-HYDROXYPROPANE-1,2-DIYLDIHE... (4AGa)
2a: (1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-... (5PLa)
2b: (1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-... (5PLb)
3a: (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETR... (7E8a)
3b: (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETR... (7E8b)
4a: 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRA... (7E9a)
5a: CHLORIDE ION (CLa)
5b: CHLORIDE ION (CLb)
5c: CHLORIDE ION (CLc)
7a: DINUCLEAR COPPER ION (CUAa)
7b: DINUCLEAR COPPER ION (CUAb)
6a: COPPER (II) ION (CUa)
7b: COPPER (II) ION (CUb)
8a: N-FORMYLMETHIONINE (FMEa)
8b: N-FORMYLMETHIONINE (FMEb)
9a: HEME-AS (HASa)
9b: HEME-AS (HASb)
9c: HEME-AS (HASc)
9d: HEME-AS (HASd)
10a: HEME C (HECa)
10b: HEME C (HECb)
11a: MAGNESIUM ION (MGa)
11b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4AG
-1
Ligand/Ion
(2R)-3-HYDROXYPROPANE-1,2-DIYLDIHEXADECANOATE
2
5PL
1
Ligand/Ion
(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE
3
7E8
-1
Ligand/Ion
(2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE
4
7E9
-1
Ligand/Ion
1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE
5
CL
-1
Ligand/Ion
CHLORIDE ION
6
CU
-1
Ligand/Ion
COPPER (II) ION
7
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
8
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
9
HAS
2
Ligand/Ion
HEME-AS
10
HEC
1
Ligand/Ion
HEME C
11
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(10, 10)
Info
All Sites
01: BC2 (SOFTWARE)
02: BC4 (SOFTWARE)
03: BC5 (SOFTWARE)
04: BC6 (SOFTWARE)
05: BC7 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
BC2
SOFTWARE
PHE A:665 , HOH B:2090 , LEU D:657 , TRP D:658 , LEU D:661 , LEU D:662 , PHE D:665
BINDING SITE FOR RESIDUE 7E9 B 701
02
BC4
SOFTWARE
LEU D:106 , ARG D:108 , PHE D:165 , LEU D:169 , ALA D:590 , LEU D:593 , TRP D:596 , ALA D:597 , ASP D:600 , GLU D:601 , GLU D:628 , LEU D:738 , ILE D:742 , PHE D:745 , GLY D:746 , GLN D:753 , LYS D:758 , GLY D:765 , THR D:766 , ALA D:769 , TYR D:773 , HOH D:2020 , HOH D:2093 , HOH D:2096 , HOH D:2111
BINDING SITE FOR RESIDUE 5PL D 900
03
BC5
SOFTWARE
PHE D:37 , PHE D:39 , ALA D:40 , GLY D:43 , SER D:46 , ILE D:49 , ARG D:50 , TYR D:66 , LEU D:70 , HIS D:73 , MET D:77 , LEU D:78 , GLY D:138 , TRP D:139 , TYR D:380 , PHE D:386 , HIS D:387 , MET D:391 , PHE D:434 , GLN D:437 , ARG D:447 , ARG D:448 , TYR D:449 , LEU D:473 , HOH D:2012 , HOH D:2082
BINDING SITE FOR RESIDUE HAS D1015
04
BC6
SOFTWARE
TRP D:139 , TRP D:246 , VAL D:253 , TYR D:254 , HIS D:299 , HIS D:300 , THR D:318 , ILE D:321 , ALA D:322 , GLY D:326 , LEU D:358 , GLY D:361 , ILE D:362 , GLY D:364 , VAL D:365 , LEU D:367 , SER D:368 , ASP D:373 , HIS D:377 , VAL D:382 , HIS D:385 , PHE D:386 , VAL D:389 , LEU D:390 , SER D:394 , ARG D:447 , HOH D:2054 , HOH D:2067 , HOH D:2074 , HOH D:2075 , HOH D:2083 , PHE E:45 , ILE E:49 , PRO E:91 , LEU E:98
BINDING SITE FOR RESIDUE HAS D1016
05
BC7
SOFTWARE
HIS D:250 , HIS D:299 , HIS D:300 , HOH D:2053 , HOH D:2054
BINDING SITE FOR RESIDUE CU D1017
06
BC8
SOFTWARE
SER D:771 , HIS D:775
BINDING SITE FOR RESIDUE CL D1701
07
BC9
SOFTWARE
HIS D:377 , ASP D:378 , HOH D:2027 , HOH D:2070 , HOH D:2076 , GLU E:199
BINDING SITE FOR RESIDUE MG D1801
08
CC1
SOFTWARE
HIS E:162 , CYS E:197 , GLU E:199 , CYS E:201 , HIS E:205 , MET E:208
BINDING SITE FOR RESIDUE CUA E 585
09
CC2
SOFTWARE
PRO B:307 , PHE E:126 , TRP E:127 , ASN E:141 , ASN E:246 , CYS E:247 , CYS E:250 , HIS E:251 , PRO E:264 , TRP E:269 , ARG E:272 , LEU E:275 , GLY E:276 , ALA E:277 , LEU E:287 , TRP E:290 , ILE E:291 , LYS E:298 , VAL E:301 , MET E:303 , PRO E:304 , PHE E:306 , LEU E:317 , HOH E:2004 , HOH E:2008 , HOH E:2030
BINDING SITE FOR RESIDUE HEC E 587
10
CC3
SOFTWARE
THR D:308
BINDING SITE FOR RESIDUE CL F 101
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: COX1_CUB (D:246-300)
2: COX3 (D:545-791)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX13_THET8
246-300
1
-
D:246-300
2
COX3
PS50253
Heme-copper oxidase subunit III family profile.
COX13_THET8
545-791
1
-
D:545-791
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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CATH Domains
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all CATH domains
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Sorry, no Info available
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Pfam Domains
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Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Chain E
Chain F
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (815 KB)
Header - Asym.Unit
Biol.Unit 1 (404 KB)
Header - Biol.Unit 1
Biol.Unit 2 (403 KB)
Header - Biol.Unit 2
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