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3WGV
Biol. Unit 2
Info
Asym.Unit (932 KB)
Biol.Unit 1 (460 KB)
Biol.Unit 2 (463 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A NA+-BOUND NA+,K+-ATPASE PRECEDING THE E1P STATE WITH OLIGOMYCIN
Authors
:
R. Kanai, H. Ogawa, B. Vilsen, F. Cornelius, C. Toyoshima
Date
:
09 Aug 13 (Deposition) - 09 Oct 13 (Release) - 16 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,G
Biol. Unit 1: A,B,G (1x)
Biol. Unit 2: C,D,E (1x)
Keywords
:
Membrane Protein, Ion Pump, Atpase, Na+ Binding, Haloacid Dehydrogenease Superfamily, Phosphate Analogue, Atp-Binding, Hydrolase, Ion Transport, Nucleotide-Binding, Phosphoprotein, Hydrolase-Transport Protein-Antibiotic Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
R. Kanai, H. Ogawa, B. Vilsen, F. Cornelius, C. Toyoshima
Crystal Structure Of A Na1-Bound Na1, K1-Atpase Preceding Th E1P State
Nature V. 502 201 2013
[
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: TETRAFLUOROALUMINATE ION (ALFa)
2b: TETRAFLUOROALUMINATE ION (ALFb)
3a: CHOLESTEROL (CLRa)
3b: CHOLESTEROL (CLRb)
3c: CHOLESTEROL (CLRc)
3d: CHOLESTEROL (CLRd)
3e: CHOLESTEROL (CLRe)
3f: CHOLESTEROL (CLRf)
4a: OLIGOMYCIN A (EFOa)
4b: OLIGOMYCIN A (EFOb)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
6c: SODIUM ION (NAc)
6d: SODIUM ION (NAd)
6e: SODIUM ION (NAe)
6f: SODIUM ION (NAf)
6g: SODIUM ION (NAg)
7h: SODIUM ION (NAh)
8a: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1a)
8b: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1b)
8c: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1c)
8d: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1d)
8e: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1e)
8f: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1f)
8g: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1g)
8h: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1h)
8i: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1i)
8j: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHO... (PC1j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ALF
1
Ligand/Ion
TETRAFLUOROALUMINATE ION
3
CLR
3
Ligand/Ion
CHOLESTEROL
4
EFO
1
Ligand/Ion
OLIGOMYCIN A
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NA
-1
Ligand/Ion
SODIUM ION
7
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
PC1
5
Ligand/Ion
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
[
close Hetero Component info
]
Sites
(22, 22)
Info
All Sites
01: BC1 (SOFTWARE)
02: BC4 (SOFTWARE)
03: BC7 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC4 (SOFTWARE)
18: DC5 (SOFTWARE)
19: DC6 (SOFTWARE)
20: DC7 (SOFTWARE)
21: DC8 (SOFTWARE)
22: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC1
SOFTWARE
PHE A:860 , GLU A:868 , THR A:979 , PHE A:982 , CYS A:983 , PRO A:986 , THR B:53 , VAL B:56 , PC1 C:2011
BINDING SITE FOR RESIDUE CLR A 2010
02
BC4
SOFTWARE
GLN A:939 , VAL A:993 , GLU A:996 , ARG A:1003 , PC1 B:401 , THR C:979 , PHE C:982 , PC1 C:2011 , THR D:60 , CLR D:3002 , PC1 D:3003
BINDING SITE FOR RESIDUE PC1 A 2013
03
BC7
SOFTWARE
PHE A:982 , PC1 A:2013 , THR B:60 , TYR B:68 , VAL C:937 , PHE C:938 , GLN C:940 , GLY C:941 , MET C:942 , LYS C:943 , PHE C:952 , PHE C:985 , SER C:988 , LEU C:989 , PHE C:992 , CLR E:101
BINDING SITE FOR RESIDUE PC1 B 401
04
BC9
SOFTWARE
TYR A:963 , TRP A:981 , PHE A:985 , PC1 D:3003 , VAL G:26 , GLY G:30 , PHE G:33
BINDING SITE FOR RESIDUE CLR G 101
05
CC1
SOFTWARE
ALF C:2002 , ADP C:2004 , HOH C:2102
BINDING SITE FOR RESIDUE MG C 2001
06
CC2
SOFTWARE
ASP C:369 , LYS C:370 , THR C:371 , THR C:610 , GLY C:611 , LYS C:691 , ASN C:713 , MG C:2001 , MG C:2003 , ADP C:2004
BINDING SITE FOR RESIDUE ALF C 2002
07
CC3
SOFTWARE
ASP C:369 , THR C:371 , ASP C:710 , ALF C:2002 , HOH C:2102
BINDING SITE FOR RESIDUE MG C 2003
08
CC4
SOFTWARE
THR C:371 , ASP C:443 , GLU C:446 , PHE C:475 , SER C:477 , LYS C:480 , TYR C:481 , GLN C:482 , LYS C:501 , GLY C:502 , ALA C:503 , ARG C:544 , VAL C:545 , LEU C:546 , THR C:610 , GLY C:611 , ASP C:612 , ARG C:685 , ASN C:713 , MG C:2001 , ALF C:2002
BINDING SITE FOR RESIDUE ADP C 2004
09
CC5
SOFTWARE
VAL C:322 , ALA C:323 , ASN C:324 , VAL C:325 , GLU C:327 , ASP C:804 , NA C:2006
BINDING SITE FOR RESIDUE NA C 2005
10
CC6
SOFTWARE
ALA C:323 , THR C:772 , SER C:775 , ASN C:776 , GLU C:779 , ASP C:804 , ASP C:808 , NA C:2005 , HOH C:2101
BINDING SITE FOR RESIDUE NA C 2006
11
CC7
SOFTWARE
TYR C:771 , THR C:772 , THR C:774 , SER C:775 , ASP C:808 , GLN C:923
BINDING SITE FOR RESIDUE NA C 2007
12
CC8
SOFTWARE
LYS C:719 , ASP C:740 , HOH C:2106 , HOH C:2107
BINDING SITE FOR RESIDUE NA C 2008
13
CC9
SOFTWARE
ILE C:287 , LYS C:836 , VAL C:838 , ASN C:839 , GLU C:840 , ILE C:843 , TYR C:847 , PC1 C:2012
BINDING SITE FOR RESIDUE PC1 C 2009
14
DC1
SOFTWARE
VAL C:128 , PHE C:139 , TYR C:142 , GLN C:143 , CYS C:802 , LEU C:805 , MET C:809 , TYR C:817
BINDING SITE FOR RESIDUE PC1 C 2010
15
DC2
SOFTWARE
CLR A:2010 , PC1 A:2013 , VAL B:56 , SER C:936 , PHE C:938 , VAL C:993 , GLU C:996 , LEU C:1000 , ARG C:1003 , CLR D:3002
BINDING SITE FOR RESIDUE PC1 C 2011
16
DC3
SOFTWARE
HIS C:283 , GLU C:840 , PC1 C:2009 , TRP D:12
BINDING SITE FOR RESIDUE PC1 C 2012
17
DC4
SOFTWARE
ARG C:87 , PHE C:90 , GLY C:92 , MET C:95 , ILE C:285 , GLU C:355
BINDING SITE FOR RESIDUE EFO C 2013
18
DC5
SOFTWARE
THR C:781 , GLU C:840 , ARG D:27 , ILE D:35 , TYR D:39 , TYR D:43
BINDING SITE FOR RESIDUE CLR D 3001
19
DC6
SOFTWARE
PC1 A:2013 , PHE C:860 , GLU C:868 , THR C:979 , PRO C:986 , PC1 C:2011 , THR D:53 , VAL D:56 , MET D:57
BINDING SITE FOR RESIDUE CLR D 3002
20
DC7
SOFTWARE
TRP A:924 , PHE A:938 , MET A:942 , PHE A:952 , THR A:955 , PHE A:985 , SER A:988 , LEU A:989 , PC1 A:2013 , LYS C:977 , PRO C:978 , TYR D:68 , TYR E:21 , PHE G:33 , CLR G:101
BINDING SITE FOR RESIDUE PC1 D 3003
21
DC8
SOFTWARE
ASN D:158
BINDING SITE FOR RESIDUE NAG D 3004
22
DC9
SOFTWARE
PC1 B:401 , TRP C:924 , TYR C:963 , TRP C:981 , PHE C:985 , VAL E:26 , GLY E:29 , GLY E:30 , PHE E:33
BINDING SITE FOR RESIDUE CLR E 101
[
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]
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
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: ATPASE_NA_K_BETA_1 (D:12-32)
2: ATPASE_NA_K_BETA_2 (D:146-161)
3: ATPASE_E1_E2 (C:369-375)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_NA_K_BETA_1
PS00390
Sodium and potassium ATPases beta subunits signature 1.
AT1B1_PIG
12-32
1
-
D:12-32
2
ATPASE_NA_K_BETA_2
PS00391
Sodium and potassium ATPases beta subunits signature 2.
AT1B1_PIG
146-161
1
-
D:146-161
3
ATPASE_E1_E2
PS00154
E1-E2 ATPases phosphorylation site.
AT1A1_PIG
374-380
1
-
C:369-375
[
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]
Exons
(0, 0)
Info
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All Exon Boundaries
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
[
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