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1Q99
Biol. Unit 2
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Asym.Unit (130 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE SR PROTEIN KINSAE, SKY1P, COMPLEXED WITH THE NON-HYDROLYZABLE ATP ANALOGUE, AMP-PNP
Authors
:
B. Nolen, J. Ngo, S. Chakrabarti, D. Vu, J. A. Adams, G. Ghosh
Date
:
22 Aug 03 (Deposition) - 23 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.11
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
B. Nolen, J. Ngo, S. Chakrabarti, D. Vu, J. A. Adams, G. Ghosh
Nucleotide-Induced Conformational Changes In The Saccharomyces Cerevisiae Sr Protein Kinase, Sky1P, Revealed By X-Ray Crystallography
Biochemistry V. 42 9575 2003
(for further references see the
PDB file header
)
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Hetero Components
(4, 4)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: METHANOL (MOHa)
3b: METHANOL (MOHb)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
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Label:
No.
Name
Count
Type
Full Name
1
ANP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
MOH
1
Ligand/Ion
METHANOL
4
NI
-1
Ligand/Ion
NICKEL (II) ION
5
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(6, 6)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
HIS B:145 , GLU B:151 , TYR B:153 , HIS B:234
BINDING SITE FOR RESIDUE NI B 363
2
AC4
SOFTWARE
TYR B:153 , LYS B:154 , ASP B:155 , ASN B:233 , HIS B:234 , LYS B:235 , HOH B:2007
BINDING SITE FOR RESIDUE SO4 B 802
3
AC6
SOFTWARE
TRP B:166 , GLY B:167 , HIS B:168 , PHE B:169 , SER B:170 , VAL B:172 , ALA B:185 , LYS B:187 , LEU B:226 , GLU B:247 , LEU B:249 , ASP B:550 , ASN B:553 , HOH B:2051 , HOH B:2109
BINDING SITE FOR RESIDUE ANP B 902
4
AC7
SOFTWARE
HOH A:2048 , ALA B:198 , ASP B:201 , TYR B:561 , MOH B:2000 , HOH B:2008
BINDING SITE FOR RESIDUE EDO B 1439
5
AC9
SOFTWARE
MOH A:2001 , EDO B:1439
BINDING SITE FOR RESIDUE MOH B 2000
6
BC1
SOFTWARE
EDO A:1440 , GLU B:197 , MOH B:2000
BINDING SITE FOR RESIDUE MOH A 2001
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (B:164-187)
2: PROTEIN_KINASE_ST (B:290-302)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
SKY1_YEAST
164-187
1
-
B:164-187
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
SKY1_YEAST
290-302
1
-
B:290-302
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Exons
(0, 0)
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1q99a_ (A:)
1b: SCOP_d1q99b_ (B:)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
Sky1p
(5)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
1a
d1q99a_
A:
1b
d1q99b_
B:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1q99A01 (A:144-211,A:226-248)
1b: CATH_1q99B01 (B:144-211,B:226-248)
2a: CATH_1q99A02 (A:212-225,A:249-735)
2b: CATH_1q99B02 (B:212-225,B:249-735)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Baker's yeast (Saccharomyces cerevisiae)
(32)
1a
1q99A01
A:144-211,A:226-248
1b
1q99B01
B:144-211,B:226-248
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Baker's yeast (Saccharomyces cerevisiae)
(21)
2a
1q99A02
A:212-225,A:249-735
2b
1q99B02
B:212-225,B:249-735
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Pkinase_1q99B01 (B:539-706)
1b: PFAM_Pkinase_1q99B02 (B:539-706)
1c: PFAM_Pkinase_1q99B03 (B:539-706)
1d: PFAM_Pkinase_1q99B04 (B:539-706)
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Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(15)
1a
Pkinase-1q99B01
B:539-706
1b
Pkinase-1q99B02
B:539-706
1c
Pkinase-1q99B03
B:539-706
1d
Pkinase-1q99B04
B:539-706
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Chain B
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (130 KB)
Header - Asym.Unit
Biol.Unit 1 (63 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
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