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3KDP
Biol. Unit 2
Info
Asym.Unit (914 KB)
Biol.Unit 1 (456 KB)
Biol.Unit 2 (456 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SODIUM-POTASSIUM PUMP
Authors
:
J. P. Morth, B. P. Pedersen, P. Nissen
Date
:
23 Oct 09 (Deposition) - 16 Feb 10 (Release) - 15 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,G,H
Biol. Unit 1: A,B,G (1x)
Biol. Unit 2: C,D,H (1x)
Keywords
:
Alpha Helical, Heterotrimeric Membrane Protein Complex, Atp-Binding, Hydrolase, Ion Transport, Magnesium, Membrane, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Potassium, Potassium Transport, Sodium Transport, Sodium/Potassium Transport, Transmembrane, Transport, Disulfide Bond, Glycoprotein, Signal-Anchor
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Reference
:
J. P. Morth, B. P. Pedersen, M. S. Toustrup-Jensen, T. L. Sorensen, J. Petersen, J. P. Andersen, B. Vilsen, P. Nissen
Crystal Structure Of The Sodium-Potassium Pump.
Nature V. 450 1043 2007
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: CHOLESTEROL (CLRa)
1b: CHOLESTEROL (CLRb)
2a: TETRAFLUOROMAGNESATE(2-) (MF4a)
2b: TETRAFLUOROMAGNESATE(2-) (MF4b)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: RUBIDIUM ION (RBa)
4b: RUBIDIUM ION (RBb)
4c: RUBIDIUM ION (RBc)
4d: RUBIDIUM ION (RBd)
4e: RUBIDIUM ION (RBe)
4f: RUBIDIUM ION (RBf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CLR
1
Ligand/Ion
CHOLESTEROL
2
MF4
1
Ligand/Ion
TETRAFLUOROMAGNESATE(2-)
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
RB
-1
Ligand/Ion
RUBIDIUM ION
[
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Sites
(6, 6)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
THR C:212 , GLY C:213 , GLU C:214 , ASP C:369 , LYS C:370 , THR C:371 , THR C:610 , GLY C:611 , LYS C:691 , ASN C:713 , MG C:2002
BINDING SITE FOR RESIDUE MF4 C 2001
2
AC8
SOFTWARE
ASP C:369 , THR C:371 , ASP C:710 , MF4 C:2001
BINDING SITE FOR RESIDUE MG C 2002
3
AC9
SOFTWARE
THR C:772 , SER C:775 , ASN C:776 , GLU C:779 , ASP C:804
BINDING SITE FOR RESIDUE RB C 2003
4
BC1
SOFTWARE
VAL C:322 , VAL C:325 , GLU C:327 , ASN C:776 , GLU C:779 , ASP C:804
BINDING SITE FOR RESIDUE RB C 2004
5
BC2
SOFTWARE
ALA C:721 , ASP C:740
BINDING SITE FOR RESIDUE RB C 2005
6
BC3
SOFTWARE
MET C:852 , TYR D:39 , TYR D:43
BINDING SITE FOR RESIDUE CLR D 3001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ATPASE_NA_K_BETA_2 (D:146-161)
2: ATPASE_E1_E2 (C:369-375)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_NA_K_BETA_2
PS00391
Sodium and potassium ATPases beta subunits signature 2.
AT1B1_PIG
146-161
1
-
D:146-161
2
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
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(5, 10)
Info
all CATH domains
1a: CATH_3kdpA04 (A:377-587)
1b: CATH_3kdpC04 (C:377-587)
2a: CATH_3kdpA03 (A:364-376,A:588-748)
2b: CATH_3kdpC03 (C:364-376,C:588-748)
3a: CATH_3kdpA02 (A:87-140,A:270-363,A:749-1016)
3b: CATH_3kdpC02 (C:87-140,C:270-363,C:749-1016)
4a: CATH_3kdpA01 (A:19-70,A:150-269)
4b: CATH_3kdpC01 (C:19-70,C:150-269)
5a: CATH_3kdpB02 (B:62-303)
5b: CATH_3kdpD02 (D:62-303)
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)
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)
(
)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Calcium-transporting ATPase, cytoplasmic domain N
(43)
Homologous Superfamily
:
Calcium-transporting ATPase, cytoplasmic domain N
(43)
Pig (Sus scrofa)
(3)
1a
3kdpA04
A:377-587
1b
3kdpC04
C:377-587
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1000, no name defined]
(211)
Pig (Sus scrofa)
(2)
2a
3kdpA03
A:364-376,A:588-748
2b
3kdpC03
C:364-376,C:588-748
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Calcium-transporting ATPase, transmembrane domain
(36)
Homologous Superfamily
:
Calcium-transporting ATPase, transmembrane domain
(36)
Pig (Sus scrofa)
(2)
3a
3kdpA02
A:87-140,A:270-363,A:749-1016
3b
3kdpC02
C:87-140,C:270-363,C:749-1016
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Calcium-transporting ATPase, cytoplasmic transduction domain A
(35)
Homologous Superfamily
:
Calcium-transporting ATPase, cytoplasmic transduction domain A
(35)
Pig (Sus scrofa)
(2)
4a
3kdpA01
A:19-70,A:150-269
4b
3kdpC01
C:19-70,C:150-269
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Na, k-atpase alpha subunit.
(3)
Pig (Sus scrofa)
(1)
5a
3kdpB02
B:62-303
5b
3kdpD02
D:62-303
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Pfam Domains
(6, 12)
Info
all PFAM domains
1a: PFAM_Hydrolase_3kdpC01 (C:363-722)
1b: PFAM_Hydrolase_3kdpC02 (C:363-722)
2a: PFAM_ATP1G1_PLM_MAT8_3kdpH01 (H:23-49)
2b: PFAM_ATP1G1_PLM_MAT8_3kdpH02 (H:23-49)
3a: PFAM_Cation_ATPase_C_3kdpC03 (C:792-1001)
3b: PFAM_Cation_ATPase_C_3kdpC04 (C:792-1001)
4a: PFAM_Cation_ATPase_N_3kdpC05 (C:36-104)
4b: PFAM_Cation_ATPase_N_3kdpC06 (C:36-104)
5a: PFAM_E1_E2_ATPase_3kdpC07 (C:128-359)
5b: PFAM_E1_E2_ATPase_3kdpC08 (C:128-359)
6a: PFAM_Na_K_ATPase_3kdpD01 (D:18-298)
6b: PFAM_Na_K_ATPase_3kdpD02 (D:18-298)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
Hydrolase
(64)
Sus scrofa (Pig)
(3)
1a
Hydrolase-3kdpC01
C:363-722
1b
Hydrolase-3kdpC02
C:363-722
Clan
:
no clan defined [family: ATP1G1_PLM_MAT8]
(5)
Family
:
ATP1G1_PLM_MAT8
(5)
Sus scrofa (Pig)
(2)
2a
ATP1G1_PLM_MAT8-3kdpH01
H:23-49
2b
ATP1G1_PLM_MAT8-3kdpH02
H:23-49
Clan
:
no clan defined [family: Cation_ATPase_C]
(21)
Family
:
Cation_ATPase_C
(21)
Sus scrofa (Pig)
(3)
3a
Cation_ATPase_C-3kdpC03
C:792-1001
3b
Cation_ATPase_C-3kdpC04
C:792-1001
Clan
:
no clan defined [family: Cation_ATPase_N]
(22)
Family
:
Cation_ATPase_N
(22)
Sus scrofa (Pig)
(3)
4a
Cation_ATPase_N-3kdpC05
C:36-104
4b
Cation_ATPase_N-3kdpC06
C:36-104
Clan
:
no clan defined [family: E1-E2_ATPase]
(23)
Family
:
E1-E2_ATPase
(23)
Sus scrofa (Pig)
(3)
5a
E1-E2_ATPase-3kdpC07
C:128-359
5b
E1-E2_ATPase-3kdpC08
C:128-359
Clan
:
no clan defined [family: Na_K-ATPase]
(3)
Family
:
Na_K-ATPase
(3)
Sus scrofa (Pig)
(3)
6a
Na_K-ATPase-3kdpD01
D:18-298
6b
Na_K-ATPase-3kdpD02
D:18-298
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