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3JU5
Asym. Unit
Info
Asym.Unit (278 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (136 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIMERIC ARGININE KINASE AT 1.75-A RESOLUTION
Authors
:
X. Wu, S. Ye, S. Guo, W. Yan, M. Bartlam, Z. Rao
Date
:
14 Sep 09 (Deposition) - 29 Sep 09 (Release) - 19 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Arginine Kinase, Reciprocating Mechanism, Negative Cooperativity, Phosphagen Kinase, Atp-Binding, Kinase, Nucleotide-Binding, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Wu, S. Ye, S. Guo, W. Yan, M. Bartlam, Z. Rao
Structural Basis For A Reciprocating Mechanism Of Negative Cooperativity In Dimeric Phosphagen Kinase Activity
Faseb J. V. 24 242 2010
(for further references see the
PDB file header
)
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Hetero Components
(2, 54)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
MSE
52
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:2 , ARG A:50 , HOH A:1139 , HOH B:1007
BINDING SITE FOR RESIDUE MG A 371
2
AC2
SOFTWARE
ALA C:2 , ARG C:50 , HOH C:414
BINDING SITE FOR RESIDUE MG C 371
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: PHOSPHAGEN_KINASE_N (A:6-89,B:6-89,C:6-89,D:6-89)
2: PHOSPHAGEN_KINASE_C (A:115-358,B:115-358,C:115-358,D:11...)
3: PHOSPHAGEN_KINASE (A:274-280,B:274-280,C:274-280,D:27...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHAGEN_KINASE_N
PS51509
Phosphagen kinase N-terminal domain profile.
KARG_STIJA
6-89
4
A:6-89
B:6-89
C:6-89
D:6-89
2
PHOSPHAGEN_KINASE_C
PS51510
Phosphagen kinase C-terminal domain profile.
KARG_STIJA
115-358
4
A:115-358
B:115-358
C:115-358
D:115-358
3
PHOSPHAGEN_KINASE
PS00112
Phosphagen kinase active site signature.
KARG_STIJA
274-280
4
A:274-280
B:274-280
C:274-280
D:274-280
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3ju5a1 (A:2-93)
1b: SCOP_d3ju5b1 (B:2-93)
1c: SCOP_d3ju5c1 (C:2-93)
1d: SCOP_d3ju5d1 (D:2-93)
2a: SCOP_d3ju5a2 (A:94-370)
2b: SCOP_d3ju5b2 (B:94-370)
2c: SCOP_d3ju5c2 (C:94-370)
2d: SCOP_d3ju5d2 (D:94-370)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Guanido kinase N-terminal domain
(35)
Superfamily
:
Guanido kinase N-terminal domain
(35)
Family
:
Guanido kinase N-terminal domain
(21)
Protein domain
:
Arginine kinase, N-domain
(13)
Apostichopus japonicus [TaxId: 307972]
(2)
1a
d3ju5a1
A:2-93
1b
d3ju5b1
B:2-93
1c
d3ju5c1
C:2-93
1d
d3ju5d1
D:2-93
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Glutamine synthetase/guanido kinase
(68)
Superfamily
:
Glutamine synthetase/guanido kinase
(68)
Family
:
Guanido kinase catalytic domain
(29)
Protein domain
:
Arginine kinase, C-terminal domain
(13)
Apostichopus japonicus [TaxId: 307972]
(2)
2a
d3ju5a2
A:94-370
2b
d3ju5b2
B:94-370
2c
d3ju5c2
C:94-370
2d
d3ju5d2
D:94-370
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3ju5A01 (A:2-93)
1b: CATH_3ju5B01 (B:2-93)
1c: CATH_3ju5C01 (C:2-93)
1d: CATH_3ju5D01 (D:2-93)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase Creatine Kinase; Chain A, domain 1
(26)
Homologous Superfamily
:
Transferase Creatine Kinase, Chain A, domain 1
(26)
Sea cucumber (Apostichopus japonicus)
(2)
1a
3ju5A01
A:2-93
1b
3ju5B01
B:2-93
1c
3ju5C01
C:2-93
1d
3ju5D01
D:2-93
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_ATP_gua_Ptrans_3ju5D01 (D:110-358)
1b: PFAM_ATP_gua_Ptrans_3ju5D02 (D:110-358)
1c: PFAM_ATP_gua_Ptrans_3ju5D03 (D:110-358)
1d: PFAM_ATP_gua_Ptrans_3ju5D04 (D:110-358)
2a: PFAM_ATP_gua_PtransN_3ju5D05 (D:16-91)
2b: PFAM_ATP_gua_PtransN_3ju5D06 (D:16-91)
2c: PFAM_ATP_gua_PtransN_3ju5D07 (D:16-91)
2d: PFAM_ATP_gua_PtransN_3ju5D08 (D:16-91)
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Clan
:
GCS
(23)
Family
:
ATP-gua_Ptrans
(14)
Stichopus japonicus (Sea cucumber)
(2)
1a
ATP-gua_Ptrans-3ju5D01
D:110-358
1b
ATP-gua_Ptrans-3ju5D02
D:110-358
1c
ATP-gua_Ptrans-3ju5D03
D:110-358
1d
ATP-gua_Ptrans-3ju5D04
D:110-358
Clan
:
no clan defined [family: ATP-gua_PtransN]
(14)
Family
:
ATP-gua_PtransN
(14)
Stichopus japonicus (Sea cucumber)
(2)
2a
ATP-gua_PtransN-3ju5D05
D:16-91
2b
ATP-gua_PtransN-3ju5D06
D:16-91
2c
ATP-gua_PtransN-3ju5D07
D:16-91
2d
ATP-gua_PtransN-3ju5D08
D:16-91
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