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2WPD
Asym. Unit
Info
Asym.Unit (538 KB)
Biol.Unit 1 (530 KB)
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(1)
Title
:
THE MG.ADP INHIBITED STATE OF THE YEAST F1C10 ATP SYNTHASE
Authors
:
A. Dautant, J. Velours, M. -F. Giraud
Date
:
05 Aug 09 (Deposition) - 07 Jul 10 (Release) - 06 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.43
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S (1x)
Keywords
:
Atp Phosphorylase (H+ Transporting), Atp-Binding, Central Stalk, Hydrolase, Atp Synthesis, Phosphoprotein, Membrane Protein, Lipid-Binding, Ion Transport, Nucleotide-Binding, Hydrogen Ion Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Dautant, J. Velours, M. Giraud
Crystal Structure Of The Mg. Adp-Inhibited State Of The Yeast F1C10-Atp Synthase.
J. Biol. Chem. V. 285 29502 2010
(for further references see the
PDB file header
)
[
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]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ATP
3
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
3
MG
5
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:174 , THR A:175 , GLY A:176 , LYS A:177 , THR A:178 , ALA A:179 , GLU A:330 , GLN A:432 , GLN A:434 , MG A:601 , SER D:355
BINDING SITE FOR RESIDUE ATP A 600
02
AC2
SOFTWARE
THR A:178 , ASP A:271 , ATP A:600
BINDING SITE FOR RESIDUE MG A 601
03
AC3
SOFTWARE
GLN B:174 , THR B:175 , GLY B:176 , LYS B:177 , THR B:178 , ALA B:179 , ARG B:364 , GLN B:432 , GLN B:434 , MG B:601
BINDING SITE FOR RESIDUE ATP B 600
04
AC4
SOFTWARE
LYS B:177 , THR B:178 , ASP B:271 , ATP B:600
BINDING SITE FOR RESIDUE MG B 601
05
AC5
SOFTWARE
GLN C:174 , GLY C:176 , LYS C:177 , THR C:178 , ALA C:179 , ARG C:364 , GLN C:432 , GLN C:434 , MG C:601 , SER F:355 , TYR F:368
BINDING SITE FOR RESIDUE ATP C 600
06
AC6
SOFTWARE
THR C:178 , ASP C:271 , ATP C:600
BINDING SITE FOR RESIDUE MG C 601
07
AC7
SOFTWARE
ARG C:375 , GLY D:158 , ALA D:159 , GLY D:160 , VAL D:161 , GLY D:162 , LYS D:163 , THR D:164 , VAL D:165 , TYR D:345 , PHE D:418 , MG D:601
BINDING SITE FOR RESIDUE ADP D 600
08
AC8
SOFTWARE
THR D:164 , GLU D:189 , ADP D:600
BINDING SITE FOR RESIDUE MG D 601
09
AC9
SOFTWARE
VAL B:373 , SER B:374 , ARG B:375 , GLY F:160 , GLY F:162 , LYS F:163 , THR F:164 , VAL F:165 , TYR F:345 , PHE F:418 , MG F:601
BINDING SITE FOR RESIDUE ADP F 600
10
BC1
SOFTWARE
THR F:164 , GLU F:189 , ASP F:256 , ADP F:600
BINDING SITE FOR RESIDUE MG F 601
[
close Site info
]
SAPs(SNPs)/Variants
(6, 42)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_ATP9_YEAST_001 (T46L, chain J/K/L/M/N/O/P/Q/R/S, )
2: VAR_ATP9_YEAST_002 (L53F, chain J/K/L/M/N/O/P/Q/R/S, )
3: VAR_ATP9_YEAST_003 (L57V, chain J/K/L/M/N/O/P/Q/R/S, )
4: VAR_ATP9_YEAST_004 (C65S, chain J/K/L/M/N/O/P/Q/R/S, )
5: VAR_ATPG_YEAST_001 (S174I, chain G, )
6: VAR_ATPG_YEAST_002 (S275F, chain G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_ATP9_YEAST_001
*
T
46
L
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S
T
46
L
2
UniProt
VAR_ATP9_YEAST_002
*
L
53
F
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S
L
53
F
3
UniProt
VAR_ATP9_YEAST_003
*
L
57
V
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S
L
57
V
4
UniProt
VAR_ATP9_YEAST_004
*
C
65
S
ATP9_YEAST
---
---
J/K/L/M/N/O/P/Q/R/S
C
65
S
5
UniProt
VAR_ATPG_YEAST_001
*
S
207
I
ATPG_YEAST
---
---
G
S
174
I
6
UniProt
VAR_ATPG_YEAST_002
*
S
308
F
ATPG_YEAST
---
---
G
S
275
F
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 17)
Info
All PROSITE Patterns/Profiles
1: ATPASE_C (J:38-59,K:38-59,L:38-59,M:38-59,N:...)
2: ATPASE_GAMMA (G:263-276)
3: ATPASE_ALPHA_BETA (D:346-355,E:346-355,F:346-355,A:36...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_C
PS00605
ATP synthase c subunit signature.
ATP9_YEAST
38-59
10
J:38-59
K:38-59
L:38-59
M:38-59
N:38-59
O:38-59
P:38-59
Q:38-59
R:38-59
S:38-59
2
ATPASE_GAMMA
PS00153
ATP synthase gamma subunit signature.
ATPG_YEAST
296-309
1
G:263-276
3
ATPASE_ALPHA_BETA
PS00152
ATP synthase alpha and beta subunits signature.
ATPB_YEAST
379-388
3
D:346-355
E:346-355
F:346-355
ATPA_YEAST
400-409
3
A:365-374
B:365-374
C:365-374
[
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]
Exons
(5, 9)
Info
All Exons
Exon 1.1 (A:26-510 | B:25-509 | C:26-510)
Exon 2.1 (G:1-278 (gaps))
Exon 3.1 (H:7-138)
Exon 4.1 (D:6-475 | E:6-478 | F:7-478)
Exon 5.1 (I:1-59)
View:
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Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
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
YBL099W
1
YBL099W.1
II:37050-38687
1638
ATPA_YEAST
1-545
545
3
A:26-510
B:25-509
C:26-510
485
485
485
2.1
YBR039W
1
YBR039W.1
II:315575-316510
936
ATPG_YEAST
1-311
311
1
G:1-278 (gaps)
278
3.1
YDL004W
1
YDL004W.1
IV:443027-443509
483
ATPD_YEAST
1-160
160
1
H:7-138
132
4.1
YJR121W
1
YJR121W.1
X:647597-649132
1536
ATPB_YEAST
1-511
511
3
D:6-475
E:6-478
F:7-478
470
473
472
5.1
YPL271W
1
YPL271W.1
XVI:30079-30267
189
ATP5E_YEAST
1-62
62
1
I:1-59
59
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(6, 19)
Info
all CATH domains
1a: CATH_2wpdD02 (D:83-357)
1b: CATH_2wpdA02 (A:96-381)
1c: CATH_2wpdB02 (B:96-381)
1d: CATH_2wpdC02 (C:96-381)
1e: CATH_2wpdE02 (E:83-357)
1f: CATH_2wpdF02 (F:83-357)
2a: CATH_2wpdD03 (D:358-475)
2b: CATH_2wpdE03 (E:358-478)
2c: CATH_2wpdF03 (F:358-478)
3a: CATH_2wpdG01 (G:1-25,G:237-278)
4a: CATH_2wpdB03 (B:382-509)
4b: CATH_2wpdA03 (A:382-510)
4c: CATH_2wpdC03 (C:382-510)
5a: CATH_2wpdB01 (B:25-95)
5b: CATH_2wpdA01 (A:26-95)
5c: CATH_2wpdC01 (C:26-95)
6a: CATH_2wpdF01 (F:7-82)
6b: CATH_2wpdD01 (D:6-82)
6c: CATH_2wpdE01 (E:6-82)
View:
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Classes
(
)
(
)
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)
Baker's yeast (Saccharomyces cerevisiae)
(61)
1a
2wpdD02
D:83-357
1b
2wpdA02
A:96-381
1c
2wpdB02
B:96-381
1d
2wpdC02
C:96-381
1e
2wpdE02
E:83-357
1f
2wpdF02
F:83-357
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)
Baker's yeast (Saccharomyces cerevisiae)
(3)
2a
2wpdD03
D:358-475
2b
2wpdE03
E:358-478
2c
2wpdF03
F:358-478
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.80, no name defined]
(43)
Baker's yeast (Saccharomyces cerevisiae)
(3)
3a
2wpdG01
G:1-25,G:237-278
Architecture
:
Up-down Bundle
(3216)
Topology
:
Lysin
(39)
Homologous Superfamily
:
[code=1.20.150.20, no name defined]
(33)
Baker's yeast (Saccharomyces cerevisiae)
(3)
4a
2wpdB03
B:382-509
4b
2wpdA03
A:382-510
4c
2wpdC03
C:382-510
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)
Baker's yeast (Saccharomyces cerevisiae)
(3)
5a
2wpdB01
B:25-95
5b
2wpdA01
A:26-95
5c
2wpdC01
C:26-95
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
[code=2.40.10.170, no name defined]
(33)
Baker's yeast (Saccharomyces cerevisiae)
(3)
6a
2wpdF01
F:7-82
6b
2wpdD01
D:6-82
6c
2wpdE01
E:6-82
[
close CATH info
]
Pfam Domains
(7, 31)
Info
all PFAM domains
1a: PFAM_ATP_synt_ab_N_2wpdC01 (C:26-94)
1b: PFAM_ATP_synt_ab_N_2wpdC02 (C:26-94)
1c: PFAM_ATP_synt_ab_N_2wpdC03 (C:26-94)
1d: PFAM_ATP_synt_ab_N_2wpdF01 (F:13-80)
1e: PFAM_ATP_synt_ab_N_2wpdF02 (F:13-80)
1f: PFAM_ATP_synt_ab_N_2wpdF03 (F:13-80)
2a: PFAM_ATP_synt_ab_2wpdC04 (C:150-374)
2b: PFAM_ATP_synt_ab_2wpdC05 (C:150-374)
2c: PFAM_ATP_synt_ab_2wpdC06 (C:150-374)
2d: PFAM_ATP_synt_ab_2wpdF04 (F:136-355)
2e: PFAM_ATP_synt_ab_2wpdF05 (F:136-355)
2f: PFAM_ATP_synt_ab_2wpdF06 (F:136-355)
3a: PFAM_ATP_synt_2wpdG01 (G:1-277)
4a: PFAM_ATP_synt_C_2wpdS01 (S:7-75)
4b: PFAM_ATP_synt_C_2wpdS02 (S:7-75)
4c: PFAM_ATP_synt_C_2wpdS03 (S:7-75)
4d: PFAM_ATP_synt_C_2wpdS04 (S:7-75)
4e: PFAM_ATP_synt_C_2wpdS05 (S:7-75)
4f: PFAM_ATP_synt_C_2wpdS06 (S:7-75)
4g: PFAM_ATP_synt_C_2wpdS07 (S:7-75)
4h: PFAM_ATP_synt_C_2wpdS08 (S:7-75)
4i: PFAM_ATP_synt_C_2wpdS09 (S:7-75)
4j: PFAM_ATP_synt_C_2wpdS10 (S:7-75)
5a: PFAM_ATP_synt_DE_N_2wpdH01 (H:10-90)
6a: PFAM_ATP_synt_Eps_2wpdI01 (I:1-50)
7a: PFAM_ATP_synt_ab_C_2wpdC07 (C:386-490)
7b: PFAM_ATP_synt_ab_C_2wpdC08 (C:386-490)
7c: PFAM_ATP_synt_ab_C_2wpdC09 (C:386-490)
7d: PFAM_ATP_synt_ab_C_2wpdF07 (F:368-477)
7e: PFAM_ATP_synt_ab_C_2wpdF08 (F:368-477)
7f: PFAM_ATP_synt_ab_C_2wpdF09 (F:368-477)
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Clans
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)
(
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Families
(
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(
)
Organisms
(
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(
)
Clan
:
HAS-barrel
(27)
Family
:
ATP-synt_ab_N
(27)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
1a
ATP-synt_ab_N-2wpdC01
C:26-94
1b
ATP-synt_ab_N-2wpdC02
C:26-94
1c
ATP-synt_ab_N-2wpdC03
C:26-94
1d
ATP-synt_ab_N-2wpdF01
F:13-80
1e
ATP-synt_ab_N-2wpdF02
F:13-80
1f
ATP-synt_ab_N-2wpdF03
F:13-80
Clan
:
P-loop_NTPase
(1112)
Family
:
ATP-synt_ab
(44)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(11)
2a
ATP-synt_ab-2wpdC04
C:150-374
2b
ATP-synt_ab-2wpdC05
C:150-374
2c
ATP-synt_ab-2wpdC06
C:150-374
2d
ATP-synt_ab-2wpdF04
F:136-355
2e
ATP-synt_ab-2wpdF05
F:136-355
2f
ATP-synt_ab-2wpdF06
F:136-355
Clan
:
no clan defined [family: ATP-synt]
(22)
Family
:
ATP-synt
(22)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
3a
ATP-synt-2wpdG01
G:1-277
Clan
:
no clan defined [family: ATP-synt_C]
(9)
Family
:
ATP-synt_C
(9)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
4a
ATP-synt_C-2wpdS01
S:7-75
4b
ATP-synt_C-2wpdS02
S:7-75
4c
ATP-synt_C-2wpdS03
S:7-75
4d
ATP-synt_C-2wpdS04
S:7-75
4e
ATP-synt_C-2wpdS05
S:7-75
4f
ATP-synt_C-2wpdS06
S:7-75
4g
ATP-synt_C-2wpdS07
S:7-75
4h
ATP-synt_C-2wpdS08
S:7-75
4i
ATP-synt_C-2wpdS09
S:7-75
4j
ATP-synt_C-2wpdS10
S:7-75
Clan
:
no clan defined [family: ATP-synt_DE_N]
(15)
Family
:
ATP-synt_DE_N
(15)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
5a
ATP-synt_DE_N-2wpdH01
H:10-90
Clan
:
no clan defined [family: ATP-synt_Eps]
(11)
Family
:
ATP-synt_Eps
(11)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
6a
ATP-synt_Eps-2wpdI01
I:1-50
Clan
:
no clan defined [family: ATP-synt_ab_C]
(32)
Family
:
ATP-synt_ab_C
(32)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
7a
ATP-synt_ab_C-2wpdC07
C:386-490
7b
ATP-synt_ab_C-2wpdC08
C:386-490
7c
ATP-synt_ab_C-2wpdC09
C:386-490
7d
ATP-synt_ab_C-2wpdF07
F:368-477
7e
ATP-synt_ab_C-2wpdF08
F:368-477
7f
ATP-synt_ab_C-2wpdF09
F:368-477
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