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1H8H
Asym. Unit
Info
Asym.Unit (474 KB)
Biol.Unit 1 (464 KB)
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(1)
Title
:
BOVINE MITOCHONDRIAL F1-ATPASE CRYSTALLISED IN THE PRESENCE OF 5MM AMPPNP
Authors
:
K. Braig, R. I. Menz, M. G. Montgomery, A. G. W. Leslie, J. E. Walker
Date
:
06 Feb 01 (Deposition) - 15 Apr 01 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G (1x)
Keywords
:
Atp Phosphorylase, Atp Phosphorylase (H+ Transporting), Atp Synthase, F1Fo Atp Synthase, F1-Atpase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. I. Menz, A. G. W. Leslie, J. E. Walker
The Structure And Nucleotide Occupancy Of Bovine Mitochondrial F(1)-Atpase Are Not Influenced By Crystallisation At High Concentrations Of Nucleotide
Febs Lett. V. 494 11 2001
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(5, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
2d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
3a: GLYCEROL (GOLa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
5a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ATP
4
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
GOL
1
Ligand/Ion
GLYCEROL
4
MG
5
Ligand/Ion
MAGNESIUM ION
5
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:176 , ATP A:600 , HOH A:2023 , HOH A:2024
BINDING SITE FOR RESIDUE MG A 601
02
AC2
SOFTWARE
THR B:176 , ATP B:600 , HOH B:2026
BINDING SITE FOR RESIDUE MG B 601
03
AC3
SOFTWARE
THR C:176 , ATP C:600 , HOH C:2005 , HOH C:2014
BINDING SITE FOR RESIDUE MG C 601
04
AC4
SOFTWARE
THR D:163 , ADP D:600
BINDING SITE FOR RESIDUE MG D 601
05
AC5
SOFTWARE
GLY E:159 , LYS E:162 , THR E:163
BINDING SITE FOR RESIDUE PO4 E 602
06
AC6
SOFTWARE
THR F:163 , GLU F:192 , ATP F:600 , HOH F:2008
BINDING SITE FOR RESIDUE MG F 601
07
AC7
SOFTWARE
ARG A:171 , GLN A:172 , THR A:173 , GLY A:174 , LYS A:175 , THR A:176 , SER A:177 , PHE A:357 , ARG A:362 , PRO A:363 , GLN A:430 , GLN A:432 , MG A:601 , HOH A:2023 , HOH A:2024
BINDING SITE FOR RESIDUE ATP A 600
08
AC8
SOFTWARE
ARG B:171 , GLN B:172 , THR B:173 , GLY B:174 , LYS B:175 , THR B:176 , SER B:177 , PHE B:357 , GLN B:430 , GLY B:431 , GLN B:432 , MG B:601 , HOH B:2006 , HOH B:2026 , ASP E:359
BINDING SITE FOR RESIDUE ATP B 600
09
AC9
SOFTWARE
ARG C:171 , GLN C:172 , THR C:173 , GLY C:174 , LYS C:175 , THR C:176 , SER C:177 , PHE C:357 , ARG C:362 , PRO C:363 , GLN C:430 , GLY C:431 , GLN C:432 , MG C:601 , HOH C:2014
BINDING SITE FOR RESIDUE ATP C 600
10
BC1
SOFTWARE
SER C:372 , ARG C:373 , GLY D:159 , VAL D:160 , GLY D:161 , LYS D:162 , THR D:163 , VAL D:164 , TYR D:345 , PHE D:418 , ALA D:421 , PHE D:424 , THR D:425 , MG D:601 , HOH D:2015
BINDING SITE FOR RESIDUE ADP D 600
11
BC2
SOFTWARE
ILE B:343 , SER B:344 , VAL B:371 , ARG B:373 , ALA F:158 , GLY F:159 , VAL F:160 , GLY F:161 , LYS F:162 , THR F:163 , VAL F:164 , ARG F:189 , TYR F:345 , PHE F:418 , ALA F:421 , PHE F:424 , THR F:425 , MG F:601 , HOH F:2008
BINDING SITE FOR RESIDUE ATP F 600
12
BC3
SOFTWARE
VAL B:129 , GLY B:130 , TYR B:244 , TYR B:248 , ARG B:304
BINDING SITE FOR RESIDUE GOL B 701
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 7)
Info
All PROSITE Patterns/Profiles
1: ATPASE_GAMMA (G:258-271)
2: ATPASE_ALPHA_BETA (D:346-355,E:346-355,F:346-355,A:36...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_GAMMA
PS00153
ATP synthase gamma subunit signature.
ATPG_BOVIN
283-296
1
G:258-271
2
ATPASE_ALPHA_BETA
PS00152
ATP synthase alpha and beta subunits signature.
ATPB_BOVIN
396-405
3
D:346-355
E:346-355
F:346-355
ATPA_BOVIN
406-415
3
A:363-372
B:363-372
C:363-372
[
close PROSITE info
]
Exons
(15, 33)
Info
All Exons
Exon 1.2 (D:9-63 | E:9-63 | F:9-63)
Exon 1.3 (D:63-121 | E:63-121 | F:63-121)
Exon 1.4 (D:121-162 | E:121-162 | F:121-162)
Exon 1.5 (D:162-223 | E:162-223 | F:162-223)
Exon 1.6 (D:224-276 | E:224-276 | F:224-276)
Exon 1.7 (D:277-317 | E:277-317 | F:277-317)
Exon 1.8 (D:318-388 | E:318-388 | F:318-388)
Exon 1.9 (D:389-456 | E:389-456 | F:389-456)
Exon 1.10 (D:456-475 | E:456-474 | F:456-474)
Exon 2.2 (G:1-6)
Exon 2.3 (G:6-44)
Exon 2.4 (G:77-90)
Exon 2.7 (G:209-240)
Exon 2.8 (G:240-272)
Exon 2.9 (G:272-272)
View:
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Label:
All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/-
11: Boundary 2.1/2.2
12: Boundary 2.2/2.3
13: Boundary 2.3/2.4
14: Boundary 2.4/2.5
15: Boundary 2.6/2.7
16: Boundary 2.7/2.8
17: Boundary 2.8/2.9
18: Boundary 2.9/2.10
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSBTAT00000017710
1
ENSBTAE00000144098
chr5:
61355655-61355808
154
ATPB_BOVIN
1-52
52
0
-
-
1.2
ENSBTAT00000017710
2
ENSBTAE00000144099
chr5:
61356274-61356456
183
ATPB_BOVIN
52-113
62
3
D:9-63
E:9-63
F:9-63
55
55
55
1.3
ENSBTAT00000017710
3
ENSBTAE00000144101
chr5:
61356699-61356873
175
ATPB_BOVIN
113-171
59
3
D:63-121
E:63-121
F:63-121
59
59
59
1.4
ENSBTAT00000017710
4
ENSBTAE00000144103
chr5:
61357390-61357511
122
ATPB_BOVIN
171-212
42
3
D:121-162
E:121-162
F:121-162
42
42
42
1.5
ENSBTAT00000017710
5
ENSBTAE00000144107
chr5:
61357757-61357941
185
ATPB_BOVIN
212-273
62
3
D:162-223
E:162-223
F:162-223
62
62
62
1.6
ENSBTAT00000017710
6
ENSBTAE00000144109
chr5:
61358444-61358602
159
ATPB_BOVIN
274-326
53
3
D:224-276
E:224-276
F:224-276
53
53
53
1.7
ENSBTAT00000017710
7
ENSBTAE00000144110
chr5:
61358693-61358815
123
ATPB_BOVIN
327-367
41
3
D:277-317
E:277-317
F:277-317
41
41
41
1.8
ENSBTAT00000017710
8
ENSBTAE00000144111
chr5:
61359431-61359643
213
ATPB_BOVIN
368-438
71
3
D:318-388
E:318-388
F:318-388
71
71
71
1.9
ENSBTAT00000017710
9
ENSBTAE00000144114
chr5:
61360024-61360225
202
ATPB_BOVIN
439-506
68
3
D:389-456
E:389-456
F:389-456
68
68
68
1.10
ENSBTAT00000017710
10
ENSBTAE00000297207
chr5:
61360774-61361036
263
ATPB_BOVIN
506-537
32
3
D:456-475
E:456-474
F:456-474
20
19
19
2.1
ENSBTAT00000018505
1
ENSBTAE00000150694
chr13:
14893326-14893240
87
ATPG_BOVIN
1-19
19
0
-
-
2.2
ENSBTAT00000018505
2
ENSBTAE00000150697
chr13:
14886562-14886528
35
ATPG_BOVIN
19-31
13
1
G:1-6
6
2.3
ENSBTAT00000018505
3
ENSBTAE00000150700
chr13:
14886029-14885898
132
ATPG_BOVIN
31-75
45
1
G:6-44
39
2.4
ENSBTAT00000018505
4
ENSBTAE00000150704
chr13:
14882864-14882660
205
ATPG_BOVIN
75-143
69
1
G:77-90
14
2.5
ENSBTAT00000018505
5
ENSBTAE00000150705
chr13:
14882083-14881940
144
ATPG_BOVIN
143-191
49
0
-
-
2.6
ENSBTAT00000018505
6
ENSBTAE00000150706
chr13:
14881819-14881755
65
ATPG_BOVIN
191-213
23
0
-
-
2.7
ENSBTAT00000018505
7
ENSBTAE00000150707
chr13:
14880753-14880598
156
ATPG_BOVIN
213-265
53
1
G:209-240
32
2.8
ENSBTAT00000018505
8
ENSBTAE00000150708
chr13:
14880202-14880106
97
ATPG_BOVIN
265-297
33
1
G:240-272
33
2.9
ENSBTAT00000018505
9
ENSBTAE00000305670
chr13:
14877783-14877747
37
ATPG_BOVIN
297-298
2
1
G:272-272
1
2.10
ENSBTAT00000018505
10
ENSBTAE00000305668
chr13:
14877118-14876979
140
ATPG_BOVIN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(7, 19)
Info
All SCOP Domains
1a: SCOP_d1h8ha1 (A:380-510)
1b: SCOP_d1h8hb1 (B:380-510)
1c: SCOP_d1h8hc1 (C:380-510)
2a: SCOP_d1h8hd1 (D:358-475)
2b: SCOP_d1h8he1 (E:358-474)
2c: SCOP_d1h8hf1 (F:358-474)
3a: SCOP_d1h8ha2 (A:24-94)
3b: SCOP_d1h8hb2 (B:24-94)
3c: SCOP_d1h8hc2 (C:19-94)
4a: SCOP_d1h8hd2 (D:9-81)
4b: SCOP_d1h8he2 (E:9-81)
4c: SCOP_d1h8hf2 (F:9-81)
5a: SCOP_d1h8ha3 (A:95-379)
5b: SCOP_d1h8hb3 (B:95-379)
5c: SCOP_d1h8hc3 (C:95-379)
6a: SCOP_d1h8hd3 (D:82-357)
6b: SCOP_d1h8he3 (E:82-357)
6c: SCOP_d1h8hf3 (F:82-357)
7a: SCOP_d1h8hg_ (G:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Left-handed superhelix
(73)
Superfamily
:
C-terminal domain of alpha and beta subunits of F1 ATP synthase
(55)
Family
:
C-terminal domain of alpha and beta subunits of F1 ATP synthase
(41)
Protein domain
:
F1 ATP synthase alpha subunit, domain 3
(19)
Cow (Bos taurus) [TaxId: 9913]
(15)
1a
d1h8ha1
A:380-510
1b
d1h8hb1
B:380-510
1c
d1h8hc1
C:380-510
Protein domain
:
F1 ATP synthase beta subunit, domain 3
(22)
Cow (Bos taurus) [TaxId: 9913]
(18)
2a
d1h8hd1
D:358-475
2b
d1h8he1
E:358-474
2c
d1h8hf1
F:358-474
Class
:
All beta proteins
(24004)
Fold
:
Domain of alpha and beta subunits of F1 ATP synthase-like
(89)
Superfamily
:
N-terminal domain of alpha and beta subunits of F1 ATP synthase
(55)
Family
:
N-terminal domain of alpha and beta subunits of F1 ATP synthase
(41)
Protein domain
:
F1 ATP synthase alpha subunit, domain 1
(19)
Cow (Bos taurus) [TaxId: 9913]
(15)
3a
d1h8ha2
A:24-94
3b
d1h8hb2
B:24-94
3c
d1h8hc2
C:19-94
Protein domain
:
F1 ATP synthase beta subunit, domain 1
(22)
Cow (Bos taurus) [TaxId: 9913]
(18)
4a
d1h8hd2
D:9-81
4b
d1h8he2
E:9-81
4c
d1h8hf2
F:9-81
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
RecA protein-like (ATPase-domain)
(159)
Protein domain
:
Central domain of alpha subunit of F1 ATP synthase
(19)
Cow (Bos taurus) [TaxId: 9913]
(15)
5a
d1h8ha3
A:95-379
5b
d1h8hb3
B:95-379
5c
d1h8hc3
C:95-379
Protein domain
:
Central domain of beta subunit of F1 ATP synthase
(22)
Cow (Bos taurus) [TaxId: 9913]
(18)
6a
d1h8hd3
D:82-357
6b
d1h8he3
E:82-357
6c
d1h8hf3
F:82-357
Fold
:
Pyruvate kinase C-terminal domain-like
(59)
Superfamily
:
ATP synthase (F1-ATPase), gamma subunit
(29)
Family
:
ATP synthase (F1-ATPase), gamma subunit
(22)
Protein domain
:
ATP synthase (F1-ATPase), gamma subunit
(22)
Cow (Bos taurus) [TaxId: 9913]
(19)
7a
d1h8hg_
G:
[
close SCOP info
]
CATH Domains
(5, 18)
Info
all CATH domains
1a: CATH_1h8hD02 (D:82-357)
1b: CATH_1h8hA02 (A:94-379)
1c: CATH_1h8hB02 (B:94-379)
1d: CATH_1h8hC02 (C:94-379)
1e: CATH_1h8hE02 (E:82-357)
1f: CATH_1h8hF02 (F:82-357)
2a: CATH_1h8hE03 (E:358-474)
2b: CATH_1h8hF03 (F:358-474)
2c: CATH_1h8hD03 (D:358-475)
3a: CATH_1h8hA03 (A:380-510)
3b: CATH_1h8hC03 (C:380-510)
3c: CATH_1h8hB03 (B:380-509)
4a: CATH_1h8hA01 (A:24-93)
4b: CATH_1h8hB01 (B:24-93)
4c: CATH_1h8hC01 (C:24-93)
5a: CATH_1h8hD01 (D:9-81)
5b: CATH_1h8hE01 (E:9-81)
5c: CATH_1h8hF01 (F:9-81)
View:
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Bovine (Bos taurus)
(17)
1a
1h8hD02
D:82-357
1b
1h8hA02
A:94-379
1c
1h8hB02
B:94-379
1d
1h8hC02
C:94-379
1e
1h8hE02
E:82-357
1f
1h8hF02
F:82-357
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
(32)
Homologous Superfamily
:
Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3
(32)
Bovine (Bos taurus)
(17)
2a
1h8hE03
E:358-474
2b
1h8hF03
F:358-474
2c
1h8hD03
D:358-475
Architecture
:
Up-down Bundle
(3216)
Topology
:
Lysin
(39)
Homologous Superfamily
:
[code=1.20.150.20, no name defined]
(33)
Bovine (Bos taurus)
(17)
3a
1h8hA03
A:380-510
3b
1h8hC03
C:380-510
3c
1h8hB03
B:380-509
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
[code=2.40.30.20, no name defined]
(40)
Bovine (Bos taurus)
(17)
4a
1h8hA01
A:24-93
4b
1h8hB01
B:24-93
4c
1h8hC01
C:24-93
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
[code=2.40.10.170, no name defined]
(33)
Bovine (Bos taurus)
(17)
5a
1h8hD01
D:9-81
5b
1h8hE01
E:9-81
5c
1h8hF01
F:9-81
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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select residue range 5 to 10 in all chains
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select protein & not helix & not sheet
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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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (474 KB)
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