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1Q99
Asym. Unit
Info
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)
]
)
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
(5, 10)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
MOH
2
Ligand/Ion
METHANOL
4
NI
2
Ligand/Ion
NICKEL (II) ION
5
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:145 , GLU A:151 , TYR A:153 , HIS A:234
BINDING SITE FOR RESIDUE NI A 362
02
AC2
SOFTWARE
HIS B:145 , GLU B:151 , TYR B:153 , HIS B:234
BINDING SITE FOR RESIDUE NI B 363
03
AC3
SOFTWARE
TYR A:153 , LYS A:154 , PHE A:232 , ASN A:233 , HIS A:234 , LYS A:235 , HOH A:2047 , HOH A:2052 , HOH A:2092
BINDING SITE FOR RESIDUE SO4 A 801
04
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
05
AC5
SOFTWARE
LEU A:164 , TRP A:166 , GLY A:167 , HIS A:168 , PHE A:169 , SER A:170 , VAL A:172 , LYS A:187 , LEU A:226 , GLU A:247 , LEU A:249 , ASP A:550 , ASN A:553 , HOH A:2077 , HOH A:2085
BINDING SITE FOR RESIDUE ANP A 901
06
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
07
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
08
AC8
SOFTWARE
ALA A:198 , ASP A:201 , GLY A:552 , TYR A:561 , MOH A:2001 , HOH A:2041
BINDING SITE FOR RESIDUE EDO A 1440
09
AC9
SOFTWARE
MOH A:2001 , EDO B:1439
BINDING SITE FOR RESIDUE MOH B 2000
10
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)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:164-187,B:164-187)
2: PROTEIN_KINASE_ST (A:290-302,B:290-302)
;
View:
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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
2
A:164-187
B:164-187
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
SKY1_YEAST
290-302
2
A:290-302
B:290-302
[
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:143-737 (gaps) | B:142-737 (gaps...)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YMR216C
1
YMR216C.1
XIII:701038-698810
2229
SKY1_YEAST
1-742
742
2
A:143-737 (gaps)
B:142-737 (gaps)
595
596
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1q99a_ (A:)
1b: SCOP_d1q99b_ (B:)
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(
)
(
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(
)
(
)
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(
)
(
)
Families
(
)
(
)
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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)
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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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Organisms
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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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Asymmetric Unit 1
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Asym.Unit (130 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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