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2HLD
Biol. Unit 2
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (516 KB)
Biol.Unit 2 (503 KB)
Biol.Unit 3 (486 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF YEAST MITOCHONDRIAL F1-ATPASE
Authors
:
V. Kabaleeswaran, N. Puri, J. E. Walker, A. G. Leslie, D. M. Mueller
Date
:
06 Jul 06 (Deposition) - 28 Nov 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
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,1
Biol. Unit 1: A,B,C,D,E,F,G,H,I (1x)
Biol. Unit 2: J,K,L,M,N,O,P,Q,R (1x)
Biol. Unit 3: S,T,U,V,W,X,Y,Z,1 (1x)
Keywords
:
Atp Phosphorylase (H+ Transporting), Atp Synthase, F1Fo, F1-Atpase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Kabaleeswaran, N. Puri, J. E. Walker, A. G. Leslie, D. M. Mueller
Novel Features Of The Rotary Catalytic Mechanism Revealed I The Structure Of Yeast F(1) Atpase.
Embo J. V. 25 5433 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
1e: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPe)
1f: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPf)
1g: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPg)
1h: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPh)
1i: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPi)
1j: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPj)
1k: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPk)
1l: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPl)
1m: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPm)
1n: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPn)
1o: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPo)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
3a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
5
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC6 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC6 (SOFTWARE)
10: CC7 (SOFTWARE)
11: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC6
SOFTWARE
THR J:178 , ANP J:600
BINDING SITE FOR RESIDUE MG J 700
02
AC7
SOFTWARE
THR K:178 , ANP K:600
BINDING SITE FOR RESIDUE MG K 700
03
AC8
SOFTWARE
THR L:178 , ASP L:271 , ANP L:600
BINDING SITE FOR RESIDUE MG L 700
04
AC9
SOFTWARE
THR M:164 , GLU M:189 , ANP M:600
BINDING SITE FOR RESIDUE MG M 700
05
BC1
SOFTWARE
ARG J:375 , LYS N:163 , ARG N:190 , ASP N:256 , ASN N:257 , ARG N:260
BINDING SITE FOR RESIDUE PO4 N 800
06
BC2
SOFTWARE
THR O:164 , GLU O:189 , ANP O:600
BINDING SITE FOR RESIDUE MG O 700
07
CC4
SOFTWARE
ARG J:173 , GLN J:174 , THR J:175 , GLY J:176 , LYS J:177 , THR J:178 , ALA J:179 , PHE J:359 , ARG J:364 , PRO J:365 , GLN J:432 , GLN J:434 , MG J:700 , HOH J:810
BINDING SITE FOR RESIDUE ANP J 600
08
CC5
SOFTWARE
GLN K:174 , THR K:175 , GLY K:176 , LYS K:177 , THR K:178 , ALA K:179 , PHE K:359 , ARG K:364 , GLN K:432 , GLN K:434 , MG K:700
BINDING SITE FOR RESIDUE ANP K 600
09
CC6
SOFTWARE
ARG L:173 , GLN L:174 , THR L:175 , GLY L:176 , LYS L:177 , THR L:178 , ALA L:179 , PHE L:359 , GLN L:432 , GLN L:434 , MG L:700 , HOH L:802 , HOH L:814 , TYR O:368
BINDING SITE FOR RESIDUE ANP L 600
10
CC7
SOFTWARE
SER L:346 , SER L:374 , ARG L:375 , GLY M:158 , GLY M:160 , VAL M:161 , GLY M:162 , LYS M:163 , THR M:164 , VAL M:165 , GLU M:189 , ARG M:190 , TYR M:311 , TYR M:345 , PHE M:418 , ALA M:421 , PHE M:424 , MG M:700
BINDING SITE FOR RESIDUE ANP M 600
11
CC8
SOFTWARE
SER K:346 , VAL K:373 , ARG K:375 , GLY O:158 , ALA O:159 , GLY O:160 , VAL O:161 , GLY O:162 , LYS O:163 , THR O:164 , VAL O:165 , ARG O:190 , TYR O:345 , PHE O:418 , ALA O:421 , PHE O:424 , MG O:700
BINDING SITE FOR RESIDUE ANP O 600
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_ATPG_YEAST_001 (S174I, chain P, )
2: VAR_ATPG_YEAST_002 (S275F, chain P, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_ATPG_YEAST_001
*
S
207
I
ATPG_YEAST
---
---
P
S
174
I
2
UniProt
VAR_ATPG_YEAST_002
*
S
308
F
ATPG_YEAST
---
---
P
S
275
F
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 7)
Info
All PROSITE Patterns/Profiles
1: ATPASE_GAMMA (P:263-276)
2: ATPASE_ALPHA_BETA (M:346-355,N:346-355,O:346-355)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_GAMMA
PS00153
ATP synthase gamma subunit signature.
ATPG_YEAST
296-309
1
-
P:263-276
-
2
ATPASE_ALPHA_BETA
PS00152
ATP synthase alpha and beta subunits signature.
ATPB_YEAST
379-388
3
-
-
-
M:346-355
N:346-355
O:346-355
-
-
-
ATPA_YEAST
400-409
3
-
-
-
J:365-374
K:365-374
L:365-374
-
-
-
[
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
(4, 30)
Info
All SCOP Domains
1a: SCOP_d2hldd3 (D:358-475)
1b: SCOP_d2hldn3 (N:358-475)
1c: SCOP_d2hldo3 (O:358-474)
1d: SCOP_d2hldv3 (V:358-475)
1e: SCOP_d2hldw3 (W:358-474)
1f: SCOP_d2hldx3 (X:358-475)
1g: SCOP_d2hlde3 (E:358-475)
1h: SCOP_d2hldf3 (F:358-475)
1i: SCOP_d2hldm3 (M:358-475)
2a: SCOP_d2hldd1 (D:6-82)
2b: SCOP_d2hldn1 (N:6-82)
2c: SCOP_d2hldo1 (O:7-82)
2d: SCOP_d2hldv1 (V:6-82)
2e: SCOP_d2hldw1 (W:8-82)
2f: SCOP_d2hldx1 (X:7-82)
2g: SCOP_d2hlde1 (E:8-82)
2h: SCOP_d2hldf1 (F:7-82)
2i: SCOP_d2hldm1 (M:6-82)
3a: SCOP_d2hldd2 (D:83-357)
3b: SCOP_d2hldn2 (N:83-357)
3c: SCOP_d2hldo2 (O:83-357)
3d: SCOP_d2hldv2 (V:83-357)
3e: SCOP_d2hldw2 (W:83-357)
3f: SCOP_d2hldx2 (X:83-357)
3g: SCOP_d2hlde2 (E:83-357)
3h: SCOP_d2hldf2 (F:83-357)
3i: SCOP_d2hldm2 (M:83-357)
4a: SCOP_d2hldg_ (G:)
4b: SCOP_d2hldp_ (P:)
4c: SCOP_d2hldy_ (Y:)
View:
Select:
Label:
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
:
automated matches
(14)
Protein domain
:
automated matches
(14)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
1a
d2hldd3
D:358-475
1b
d2hldn3
N:358-475
1c
d2hldo3
O:358-474
1d
d2hldv3
V:358-475
1e
d2hldw3
W:358-474
1f
d2hldx3
X:358-475
1g
d2hlde3
E:358-475
1h
d2hldf3
F:358-475
1i
d2hldm3
M:358-475
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
:
automated matches
(14)
Protein domain
:
automated matches
(14)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
2a
d2hldd1
D:6-82
2b
d2hldn1
N:6-82
2c
d2hldo1
O:7-82
2d
d2hldv1
V:6-82
2e
d2hldw1
W:8-82
2f
d2hldx1
X:7-82
2g
d2hlde1
E:8-82
2h
d2hldf1
F:7-82
2i
d2hldm1
M:6-82
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
:
automated matches
(32)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
3a
d2hldd2
D:83-357
3b
d2hldn2
N:83-357
3c
d2hldo2
O:83-357
3d
d2hldv2
V:83-357
3e
d2hldw2
W:83-357
3f
d2hldx2
X:83-357
3g
d2hlde2
E:83-357
3h
d2hldf2
F:83-357
3i
d2hldm2
M:83-357
Fold
:
Pyruvate kinase C-terminal domain-like
(59)
Superfamily
:
ATP synthase (F1-ATPase), gamma subunit
(29)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
4a
d2hldg_
G:
4b
d2hldp_
P:
4c
d2hldy_
Y:
[
close SCOP info
]
CATH Domains
(6, 57)
Info
all CATH domains
1a: CATH_2hldD02 (D:83-357)
1b: CATH_2hldA02 (A:96-381)
1c: CATH_2hldB02 (B:96-381)
1d: CATH_2hldC02 (C:96-381)
1e: CATH_2hldJ02 (J:96-381)
1f: CATH_2hldK02 (K:96-381)
1g: CATH_2hldL02 (L:96-381)
1h: CATH_2hldS02 (S:96-381)
1i: CATH_2hldT02 (T:96-381)
1j: CATH_2hldU02 (U:96-381)
1k: CATH_2hldE02 (E:83-357)
1l: CATH_2hldF02 (F:83-357)
1m: CATH_2hldM02 (M:83-357)
1n: CATH_2hldN02 (N:83-357)
1o: CATH_2hldO02 (O:83-357)
1p: CATH_2hldV02 (V:83-357)
1q: CATH_2hldW02 (W:83-357)
1r: CATH_2hldX02 (X:83-357)
2a: CATH_2hldO03 (O:358-474)
2b: CATH_2hldW03 (W:358-474)
2c: CATH_2hldD03 (D:358-475)
2d: CATH_2hldE03 (E:358-475)
2e: CATH_2hldF03 (F:358-475)
2f: CATH_2hldM03 (M:358-475)
2g: CATH_2hldN03 (N:358-475)
2h: CATH_2hldV03 (V:358-475)
2i: CATH_2hldX03 (X:358-475)
3a: CATH_2hldG01 (G:1-25,G:237-276)
3b: CATH_2hldP01 (P:1-25,P:237-276)
3c: CATH_2hldY01 (Y:1-25,Y:237-272)
4a: CATH_2hldC03 (C:382-509)
4b: CATH_2hldA03 (A:382-509)
4c: CATH_2hldB03 (B:382-509)
4d: CATH_2hldL03 (L:382-509)
4e: CATH_2hldJ03 (J:382-509)
4f: CATH_2hldK03 (K:382-509)
4g: CATH_2hldS03 (S:382-509)
4h: CATH_2hldT03 (T:382-509)
4i: CATH_2hldU03 (U:382-509)
5a: CATH_2hldK01 (K:21-95)
5b: CATH_2hldB01 (B:25-95)
5c: CATH_2hldA01 (A:26-95)
5d: CATH_2hldC01 (C:26-95)
5e: CATH_2hldJ01 (J:26-95)
5f: CATH_2hldL01 (L:26-95)
5g: CATH_2hldT01 (T:26-95)
5h: CATH_2hldU01 (U:26-95)
5i: CATH_2hldS01 (S:27-95)
6a: CATH_2hldE01 (E:8-82)
6b: CATH_2hldW01 (W:8-82)
6c: CATH_2hldF01 (F:7-82)
6d: CATH_2hldO01 (O:7-82)
6e: CATH_2hldX01 (X:7-82)
6f: CATH_2hldD01 (D:6-82)
6g: CATH_2hldM01 (M:6-82)
6h: CATH_2hldN01 (N:6-82)
6i: CATH_2hldV01 (V:6-82)
View:
Select:
Label:
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
2hldD02
D:83-357
1b
2hldA02
A:96-381
1c
2hldB02
B:96-381
1d
2hldC02
C:96-381
1e
2hldJ02
J:96-381
1f
2hldK02
K:96-381
1g
2hldL02
L:96-381
1h
2hldS02
S:96-381
1i
2hldT02
T:96-381
1j
2hldU02
U:96-381
1k
2hldE02
E:83-357
1l
2hldF02
F:83-357
1m
2hldM02
M:83-357
1n
2hldN02
N:83-357
1o
2hldO02
O:83-357
1p
2hldV02
V:83-357
1q
2hldW02
W:83-357
1r
2hldX02
X: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
2hldO03
O:358-474
2b
2hldW03
W:358-474
2c
2hldD03
D:358-475
2d
2hldE03
E:358-475
2e
2hldF03
F:358-475
2f
2hldM03
M:358-475
2g
2hldN03
N:358-475
2h
2hldV03
V:358-475
2i
2hldX03
X:358-475
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.80, no name defined]
(43)
Baker's yeast (Saccharomyces cerevisiae)
(3)
3a
2hldG01
G:1-25,G:237-276
3b
2hldP01
P:1-25,P:237-276
3c
2hldY01
Y:1-25,Y:237-272
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
2hldC03
C:382-509
4b
2hldA03
A:382-509
4c
2hldB03
B:382-509
4d
2hldL03
L:382-509
4e
2hldJ03
J:382-509
4f
2hldK03
K:382-509
4g
2hldS03
S:382-509
4h
2hldT03
T:382-509
4i
2hldU03
U:382-509
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)
Baker's yeast (Saccharomyces cerevisiae)
(3)
5a
2hldK01
K:21-95
5b
2hldB01
B:25-95
5c
2hldA01
A:26-95
5d
2hldC01
C:26-95
5e
2hldJ01
J:26-95
5f
2hldL01
L:26-95
5g
2hldT01
T:26-95
5h
2hldU01
U:26-95
5i
2hldS01
S:27-95
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
[code=2.40.10.170, no name defined]
(33)
Baker's yeast (Saccharomyces cerevisiae)
(3)
6a
2hldE01
E:8-82
6b
2hldW01
W:8-82
6c
2hldF01
F:7-82
6d
2hldO01
O:7-82
6e
2hldX01
X:7-82
6f
2hldD01
D:6-82
6g
2hldM01
M:6-82
6h
2hldN01
N:6-82
6i
2hldV01
V:6-82
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
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Miscellaneous
Script
Example Commands
Example Command
Action
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'
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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