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2Y69
Biol. Unit 1
Info
Asym.Unit (630 KB)
Biol.Unit 1 (311 KB)
Biol.Unit 2 (312 KB)
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(1)
Title
:
BOVINE HEART CYTOCHROME C OXIDASE RE-REFINED WITH MOLECULAR OXYGEN
Authors
:
V. R. I. Kaila, E. Oksanen, A. Goldman, M. I. Verkhovsky, D. Sundholm, M.
Date
:
20 Jan 11 (Deposition) - 23 Feb 11 (Release) - 04 Feb 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,D,E,F,H,I,J,K,L,M,T (1x)
Biol. Unit 2: G,N,O,P,Q,R,S,U,V,W,X,Y,Z (1x)
Keywords
:
Electron Transport, Complex Iv, Proton Pumps, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. R. I. Kaila, E. Oksanen, A. Goldman, D. A. Bloch, M. I. Verkhovsky, D. Sundholm, M. Wikstrom
A Combined Quantum Chemical And Crystallographic Study On The Oxidized Binuclear Center Of Cytochrome C Oxidase.
Biochim. Biophys. Acta V. 1807 769 2011
[
close entry info
]
Hetero Components
(8, 12)
Info
All Hetero Components
1a: CHOLIC ACID (CHDa)
1b: CHOLIC ACID (CHDb)
1c: CHOLIC ACID (CHDc)
1d: CHOLIC ACID (CHDd)
1e: CHOLIC ACID (CHDe)
1f: CHOLIC ACID (CHDf)
3a: DINUCLEAR COPPER ION (CUAa)
3b: DINUCLEAR COPPER ION (CUAb)
2a: COPPER (II) ION (CUa)
3b: COPPER (II) ION (CUb)
4a: DECYL-BETA-D-MALTOPYRANOSIDE (DMUa)
4b: DECYL-BETA-D-MALTOPYRANOSIDE (DMUb)
5a: HEME-A (HEAa)
5b: HEME-A (HEAb)
5c: HEME-A (HEAc)
5d: HEME-A (HEAd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
7a: OXYGEN MOLECULE (OXYa)
7b: OXYGEN MOLECULE (OXYb)
8a: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKa)
8b: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)P... (PEKb)
9a: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVa)
9b: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVb)
9c: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVc)
9d: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPY... (PGVd)
10a: PHOSPHOTHREONINE (TPOa)
10b: PHOSPHOTHREONINE (TPOb)
11a: ZINC ION (ZNa)
11b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CHD
3
Ligand/Ion
CHOLIC ACID
2
CU
-1
Ligand/Ion
COPPER (II) ION
3
CUA
1
Ligand/Ion
DINUCLEAR COPPER ION
4
DMU
1
Ligand/Ion
DECYL-BETA-D-MALTOPYRANOSIDE
5
HEA
2
Ligand/Ion
HEME-A
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
OXY
1
Ligand/Ion
OXYGEN MOLECULE
8
PEK
1
Ligand/Ion
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
9
PGV
2
Ligand/Ion
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
10
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
11
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(15, 15)
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: BC5 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:28 , THR A:31 , SER A:34 , ILE A:37 , ARG A:38 , TYR A:54 , VAL A:58 , HIS A:61 , ALA A:62 , MET A:65 , ILE A:66 , MET A:69 , VAL A:70 , ILE A:73 , GLY A:125 , TRP A:126 , TYR A:371 , PHE A:377 , HIS A:378 , SER A:382 , VAL A:386 , PHE A:393 , MET A:417 , PHE A:425 , GLN A:428 , ARG A:438 , ARG A:439 , TYR A:440 , SER A:458 , VAL A:465 , MET A:468 , HOH A:2083 , HOH A:2110
BINDING SITE FOR RESIDUE HEA A 515
02
AC2
SOFTWARE
TRP A:126 , TRP A:236 , VAL A:243 , TYR A:244 , HIS A:290 , HIS A:291 , THR A:309 , THR A:316 , GLY A:317 , PHE A:348 , THR A:349 , GLY A:352 , LEU A:353 , GLY A:355 , ILE A:356 , LEU A:358 , ALA A:359 , ASP A:364 , HIS A:368 , VAL A:373 , HIS A:376 , PHE A:377 , VAL A:380 , LEU A:381 , ARG A:438 , OXY A:1515 , HOH A:2111 , HOH A:2112 , HOH A:2113
BINDING SITE FOR RESIDUE HEA A 516
03
AC3
SOFTWARE
HIS A:240 , HIS A:290 , HIS A:291 , OXY A:1515
BINDING SITE FOR RESIDUE CU A 517
04
AC4
SOFTWARE
HIS A:240 , VAL A:243 , HIS A:291 , HEA A:516 , CU A:517
BINDING SITE FOR RESIDUE OXY A1515
05
AC5
SOFTWARE
HIS A:368 , ASP A:369 , GLU B:198 , HOH B:2079 , HOH B:2089 , HOH B:2090
BINDING SITE FOR RESIDUE MG A1516
06
AC6
SOFTWARE
HIS A:233 , ASP A:300 , THR A:301 , TYR A:304 , HOH A:2114 , TRP C:99 , HIS C:103
BINDING SITE FOR RESIDUE CHD A1517
07
AC7
SOFTWARE
HIS B:161 , CYS B:196 , GLU B:198 , CYS B:200 , HIS B:204 , MET B:207
BINDING SITE FOR RESIDUE CUA B 228
08
AC8
SOFTWARE
HIS A:151 , VAL A:155 , TYR C:181 , TYR C:182 , ALA C:184 , PHE C:186 , THR C:187 , ILE C:188 , PHE C:198 , TRP G:62 , THR G:68 , PHE G:69 , PHE G:70 , HIS G:71 , ASN G:76 , HOH G:2032
BINDING SITE FOR RESIDUE PEK C1262
09
AC9
SOFTWARE
PHE A:94 , PRO A:95 , ARG A:96 , MET A:97 , MET A:100 , HOH A:2020 , HIS C:9 , ALA C:24 , ASN C:50 , MET C:54 , TRP C:57 , TRP C:58 , GLU C:64 , HIS C:71 , GLY C:82 , HOH C:2040
BINDING SITE FOR RESIDUE PGV C1263
10
BC1
SOFTWARE
TRP C:58 , VAL C:61 , SER C:65 , THR C:66 , PHE C:86 , ILE C:210 , PHE C:214 , ARG C:221 , HIS C:226 , THR C:228 , HIS C:231 , PHE C:233 , GLY C:234 , HOH C:2080 , HOH C:2085 , HOH F:2011 , HOH F:2017
BINDING SITE FOR RESIDUE PGV C1264
11
BC2
SOFTWARE
ARG C:156 , PHE C:164 , PHE C:219 , PHE J:1
BINDING SITE FOR RESIDUE CHD C1265
12
BC3
SOFTWARE
CYS F:60 , CYS F:62 , CYS F:82 , CYS F:85
BINDING SITE FOR RESIDUE ZN F1097
13
BC5
SOFTWARE
TRP D:98 , LEU M:27 , LEU M:28 , GLY M:31 , TRP M:32 , TYR M:35 , HIS M:36
BINDING SITE FOR RESIDUE DMU M1044
14
CC4
SOFTWARE
LEU N:215 , TYR P:181 , TYR P:182 , ALA P:184 , PHE P:186 , THR P:187 , ILE P:188 , PHE P:198 , PGV P:1263 , TRP T:62 , THR T:68 , PHE T:69 , PHE T:70 , HIS T:71 , ASN T:76
BINDING SITE FOR RESIDUE PEK P1262
15
CC9
SOFTWARE
MET A:271 , TRP A:275 , GLU B:62 , THR B:63 , ARG T:14 , ARG T:17 , GLY T:22
BINDING SITE FOR RESIDUE CHD T1085
[
close Site info
]
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
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(8, 8)
Info
All PROSITE Patterns/Profiles
1: COX2_TM (B:1-91)
2: COX3 (C:4-261)
3: CHCH (H:26-72)
4: COX6A (T:55-72)
5: COX2_CUA (B:92-225)
6: COX5B_1 (F:69-91)
7: COX2 (B:159-207)
8: COX1_CUB (A:236-291)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COX2_TM
PS50999
Cytochrome oxidase subunit II transmembrane region profile.
COX2_BOVIN
1-91
1
B:1-91
2
COX3
PS50253
Heme-copper oxidase subunit III family profile.
COX3_BOVIN
4-261
1
C:4-261
-
3
CHCH
PS51808
Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
CX6B1_BOVIN
27-73
1
H:26-72
-
4
COX6A
PS01329
Cytochrome c oxidase subunit VIa signature.
CX6A2_BOVIN
67-84
1
-
T:55-72
5
COX2_CUA
PS50857
Cytochrome oxidase subunit II copper A binding domain profile.
COX2_BOVIN
92-225
1
B:92-225
-
6
COX5B_1
PS00848
Cytochrome c oxidase subunit Vb, zinc binding region signature.
COX5B_BOVIN
100-122
1
F:69-91
-
7
COX2
PS00078
CO II and nitrous oxide reductase dinuclear copper centers signature.
COX2_BOVIN
159-207
1
B:159-207
-
8
COX1_CUB
PS00077
Heme-copper oxidase catalytic subunit, copper B binding region signature.
COX1_BOVIN
236-291
1
A:236-291
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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
(14, 28)
Info
All SCOP Domains
01a: SCOP_d2y69e_ (E:)
01b: SCOP_d2y69r_ (R:)
02a: SCOP_d2y69h_ (H:)
02b: SCOP_d2y69u_ (U:)
03a: SCOP_d2y69b2 (B:91-227)
03b: SCOP_d2y69o2 (O:91-227)
04a: SCOP_d2y69a_ (A:)
04b: SCOP_d2y69n_ (N:)
05a: SCOP_d2y69c_ (C:)
05b: SCOP_d2y69p_ (P:)
06a: SCOP_d2y69d_ (D:)
06b: SCOP_d2y69q_ (Q:)
07a: SCOP_d2y69g_ (G:)
07b: SCOP_d2y69t_ (T:)
08a: SCOP_d2y69i_ (I:)
08b: SCOP_d2y69v_ (V:)
09a: SCOP_d2y69j_ (J:)
09b: SCOP_d2y69w_ (W:)
10a: SCOP_d2y69k_ (K:)
10b: SCOP_d2y69x_ (X:)
11a: SCOP_d2y69l_ (L:)
11b: SCOP_d2y69y_ (Y:)
12a: SCOP_d2y69m_ (M:)
12b: SCOP_d2y69z_ (Z:)
13a: SCOP_d2y69b1 (B:1-90)
13b: SCOP_d2y69o1 (O:2-90)
14a: SCOP_d2y69f_ (F:)
14b: SCOP_d2y69s_ (S:)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
Cytochrome c oxidase subunit E
(25)
Family
:
Cytochrome c oxidase subunit E
(25)
Protein domain
:
automated matches
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
01a
d2y69e_
E:
01b
d2y69r_
R:
Fold
:
Cytochrome c oxidase subunit h
(26)
Superfamily
:
Cytochrome c oxidase subunit h
(26)
Family
:
Cytochrome c oxidase subunit h
(26)
Protein domain
:
automated matches
(18)
Cow (Bos taurus) [TaxId: 9913]
(18)
02a
d2y69h_
H:
02b
d2y69u_
U:
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)
Cow (Bos taurus) [TaxId: 9913]
(24)
03a
d2y69b2
B:91-227
03b
d2y69o2
O:91-227
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)
Cow (Bos taurus) [TaxId: 9913]
(18)
04a
d2y69a_
A:
04b
d2y69n_
N:
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
:
Mitochondrial cytochrome c oxidase, subunit III
(25)
Cow (Bos taurus) [TaxId: 9913]
(25)
05a
d2y69c_
C:
05b
d2y69p_
P:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Mitochondrial cytochrome c oxidase subunit IV
(26)
Family
:
Mitochondrial cytochrome c oxidase subunit IV
(26)
Protein domain
:
automated matches
(18)
Cow (Bos taurus) [TaxId: 9913]
(18)
06a
d2y69d_
D:
06b
d2y69q_
Q:
Superfamily
:
Mitochondrial cytochrome c oxidase subunit VIa
(25)
Family
:
Mitochondrial cytochrome c oxidase subunit VIa
(25)
Protein domain
:
automated matches
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
07a
d2y69g_
G:
07b
d2y69t_
T:
Superfamily
:
Mitochondrial cytochrome c oxidase subunit VIc
(25)
Family
:
Mitochondrial cytochrome c oxidase subunit VIc
(25)
Protein domain
:
Mitochondrial cytochrome c oxidase subunit VIc
(25)
Cow (Bos taurus) [TaxId: 9913]
(25)
08a
d2y69i_
I:
08b
d2y69v_
V:
Superfamily
:
Mitochondrial cytochrome c oxidase subunit VIIa
(25)
Family
:
Mitochondrial cytochrome c oxidase subunit VIIa
(25)
Protein domain
:
automated matches
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
09a
d2y69j_
J:
09b
d2y69w_
W:
Superfamily
:
Mitochondrial cytochrome c oxidase subunit VIIb
(26)
Family
:
Mitochondrial cytochrome c oxidase subunit VIIb
(26)
Protein domain
:
automated matches
(18)
Cow (Bos taurus) [TaxId: 9913]
(18)
10a
d2y69k_
K:
10b
d2y69x_
X:
Superfamily
:
Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
(25)
Family
:
Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
(25)
Protein domain
:
automated matches
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
11a
d2y69l_
L:
11b
d2y69y_
Y:
Superfamily
:
Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)
(26)
Family
:
Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)
(26)
Protein domain
:
automated matches
(18)
Cow (Bos taurus) [TaxId: 9913]
(18)
12a
d2y69m_
M:
12b
d2y69z_
Z:
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
:
Mitochondrial cytochrome c oxidase, subunit II
(24)
Cow (Bos taurus) [TaxId: 9913]
(24)
13a
d2y69b1
B:1-90
13b
d2y69o1
O:2-90
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Rubredoxin-like
(127)
Family
:
Cytochrome c oxidase Subunit F
(25)
Protein domain
:
automated matches
(1)
Cow (Bos taurus) [TaxId: 9913]
(1)
14a
d2y69f_
F:
14b
d2y69s_
S:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(14, 28)
Info
all PFAM domains
01a: PFAM_COX6B_2y69U01 (U:18-82)
01b: PFAM_COX6B_2y69U02 (U:18-82)
02a: PFAM_COX2_2y69O01 (O:95-214)
02b: PFAM_COX2_2y69O02 (O:95-214)
03a: PFAM_COX5B_2y69S01 (S:4-96)
03b: PFAM_COX5B_2y69S02 (S:4-96)
04a: PFAM_COX1_2y69N01 (N:12-461)
04b: PFAM_COX1_2y69N02 (N:12-461)
05a: PFAM_COX2_TM_2y69O03 (O:2-83)
05b: PFAM_COX2_TM_2y69O04 (O:2-83)
06a: PFAM_COX3_2y69P01 (P:6-261)
06b: PFAM_COX3_2y69P02 (P:6-261)
07a: PFAM_COX4_2y69Q01 (Q:4-146)
07b: PFAM_COX4_2y69Q02 (Q:4-146)
08a: PFAM_COX5A_2y69R01 (R:6-108)
08b: PFAM_COX5A_2y69R02 (R:6-108)
09a: PFAM_COX6A_2y69T01 (T:1-79)
09b: PFAM_COX6A_2y69T02 (T:1-79)
10a: PFAM_COX6C_2y69V01 (V:3-73)
10b: PFAM_COX6C_2y69V02 (V:3-73)
11a: PFAM_COX7B_2y69X01 (X:6-54)
11b: PFAM_COX7B_2y69X02 (X:6-54)
12a: PFAM_COX7C_2y69Y01 (Y:2-47)
12b: PFAM_COX7C_2y69Y02 (Y:2-47)
13a: PFAM_COX7a_2y69W01 (W:2-57)
13b: PFAM_COX7a_2y69W02 (W:2-57)
14a: PFAM_COX8_2y69Z01 (Z:1-42)
14b: PFAM_COX8_2y69Z02 (Z:1-42)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CHCH
(11)
Family
:
COX6B
(9)
Bos taurus (Bovine)
(9)
01a
COX6B-2y69U01
U:18-82
01b
COX6B-2y69U02
U:18-82
Clan
:
CU_oxidase
(192)
Family
:
COX2
(19)
Bos taurus (Bovine)
(9)
02a
COX2-2y69O01
O:95-214
02b
COX2-2y69O02
O:95-214
Clan
:
Rubredoxin
(46)
Family
:
COX5B
(10)
Bos taurus (Bovine)
(9)
03a
COX5B-2y69S01
S:4-96
03b
COX5B-2y69S02
S:4-96
Clan
:
no clan defined [family: COX1]
(19)
Family
:
COX1
(19)
Bos taurus (Bovine)
(9)
04a
COX1-2y69N01
N:12-461
04b
COX1-2y69N02
N:12-461
Clan
:
no clan defined [family: COX2_TM]
(16)
Family
:
COX2_TM
(16)
Bos taurus (Bovine)
(9)
05a
COX2_TM-2y69O03
O:2-83
05b
COX2_TM-2y69O04
O:2-83
Clan
:
no clan defined [family: COX3]
(12)
Family
:
COX3
(12)
Bos taurus (Bovine)
(9)
06a
COX3-2y69P01
P:6-261
06b
COX3-2y69P02
P:6-261
Clan
:
no clan defined [family: COX4]
(9)
Family
:
COX4
(9)
Bos taurus (Bovine)
(9)
07a
COX4-2y69Q01
Q:4-146
07b
COX4-2y69Q02
Q:4-146
Clan
:
no clan defined [family: COX5A]
(9)
Family
:
COX5A
(9)
Bos taurus (Bovine)
(9)
08a
COX5A-2y69R01
R:6-108
08b
COX5A-2y69R02
R:6-108
Clan
:
no clan defined [family: COX6A]
(9)
Family
:
COX6A
(9)
Bos taurus (Bovine)
(9)
09a
COX6A-2y69T01
T:1-79
09b
COX6A-2y69T02
T:1-79
Clan
:
no clan defined [family: COX6C]
(9)
Family
:
COX6C
(9)
Bos taurus (Bovine)
(9)
10a
COX6C-2y69V01
V:3-73
10b
COX6C-2y69V02
V:3-73
Clan
:
no clan defined [family: COX7B]
(9)
Family
:
COX7B
(9)
Bos taurus (Bovine)
(9)
11a
COX7B-2y69X01
X:6-54
11b
COX7B-2y69X02
X:6-54
Clan
:
no clan defined [family: COX7C]
(9)
Family
:
COX7C
(9)
Bos taurus (Bovine)
(9)
12a
COX7C-2y69Y01
Y:2-47
12b
COX7C-2y69Y02
Y:2-47
Clan
:
no clan defined [family: COX7a]
(9)
Family
:
COX7a
(9)
Bos taurus (Bovine)
(9)
13a
COX7a-2y69W01
W:2-57
13b
COX7a-2y69W02
W:2-57
Clan
:
no clan defined [family: COX8]
(9)
Family
:
COX8
(9)
Bos taurus (Bovine)
(9)
14a
COX8-2y69Z01
Z:1-42
14b
COX8-2y69Z02
Z:1-42
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