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2PEZ
Asym. Unit
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Asym.Unit (67 KB)
Biol.Unit 1 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTRUE OF DELETION MUTANT OF APS-KINASE DOMAIN OF HUMAN PAPS-SYNTHETASE 1 IN COMPLEX WITH CYCLIC PAPS AND DADP
Authors
:
N. Sekulic, A. Lavie
Date
:
03 Apr 07 (Deposition) - 29 May 07 (Release) - 13 May 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nmp-Kinase Fold, Protein In Complex With Nucleic Acid, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Sekulic, M. Konrad, A. Lavie
Structural Mechanism For Substrate Inhibition Of The Adenosine 5'-Phosphosulfate Kinase Domain Of Human 3'-Phosphoadenosine 5'-Phosphosulfate Synthetase 1 And Its Ramifications For Enzyme Regulation.
J. Biol. Chem. V. 282 22112 2007
(for further references see the
PDB file header
)
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE (DATa)
1b: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE (DATb)
2a: (2S,3AR,4R,6R,6AR)-4-(6-AMINO-9H-P... (GGZa)
View:
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No.
Name
Count
Type
Full Name
1
DAT
2
Ligand/Ion
2'-DEOXYADENOSINE-5'-DIPHOSPHATE
2
GGZ
1
Ligand/Ion
(2S,3AR,4R,6R,6AR)-4-(6-AMINO-9H-PURIN-9-YL)-6-({[(R)-HYDROXY(SULFOOXY)PHOSPHORYL]OXY}METHYL)TETRAHYDROFURO[3,4-D][1,3,2]DIOXAPHOSPHOL-2-OL 2-OXIDE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:61 , ARG A:92 , PHE A:101 , ARG A:106 , ASN A:109 , PHE A:131 , ILE A:132 , SER A:133 , PRO A:134 , LYS A:171 , LEU A:173 , GLY A:184 , PHE A:185 , THR A:186 , HOH A:538 , HOH A:595 , HOH A:626 , HOH A:656
BINDING SITE FOR RESIDUE GGZ A 401
2
AC2
SOFTWARE
LEU A:60 , SER A:61 , GLY A:62 , ALA A:63 , GLY A:64 , LYS A:65 , THR A:66 , THR A:67 , ARG A:168 , VAL A:170 , THR A:204 , CYS A:207 , ASP A:208 , VAL A:209 , CYS A:212 , HOH A:522 , HOH A:533 , HOH A:590 , HOH A:595 , HOH A:609 , HIS B:163 , GLN B:167
BINDING SITE FOR RESIDUE DAT A 500
3
AC3
SOFTWARE
HIS A:163 , GLN A:167 , LEU B:60 , GLY B:62 , ALA B:63 , GLY B:64 , LYS B:65 , THR B:66 , THR B:67 , ARG B:168 , VAL B:170 , THR B:204 , CYS B:207 , ASP B:208 , VAL B:209 , CYS B:212 , HOH B:616 , HOH B:653 , HOH B:658 , HOH B:701 , HOH B:704 , HOH B:713
BINDING SITE FOR RESIDUE DAT B 600
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(5, 10)
Info
All Exons
Exon 1.3 (A:51-59 | B:52-59)
Exon 1.4c (A:59-137 | B:59-137)
Exon 1.5c (A:138-184 | B:138-174)
Exon 1.6 (A:184-223 | B:191-223)
Exon 1.7b (A:224-226 | B:224-226)
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All Exon Boundaries
1: Boundary 1.1a/1.3
2: Boundary 1.3/1.4c
3: Boundary 1.4c/1.5c
4: Boundary 1.5c/1.6
5: Boundary 1.6/1.7b
6: Boundary 1.7b/1.8
View:
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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
1.1a
ENST00000265174
1a
ENSE00000935008
chr4:
108641608-108641276
333
PAPS1_HUMAN
1-20
20
0
-
-
1.3
ENST00000265174
3
ENSE00000935007
chr4:
108622441-108622327
115
PAPS1_HUMAN
21-59
39
2
A:51-59
B:52-59
9
8
1.4c
ENST00000265174
4c
ENSE00000736237
chr4:
108615162-108614927
236
PAPS1_HUMAN
59-137
79
2
A:59-137
B:59-137
79
79
1.5c
ENST00000265174
5c
ENSE00000736234
chr4:
108608333-108608195
139
PAPS1_HUMAN
138-184
47
2
A:138-184
B:138-174
47
37
1.6
ENST00000265174
6
ENSE00000736231
chr4:
108603289-108603171
119
PAPS1_HUMAN
184-223
40
2
A:184-223
B:191-223
40
33
1.7b
ENST00000265174
7b
ENSE00000841651
chr4:
108581228-108581115
114
PAPS1_HUMAN
224-261
38
2
A:224-226
B:224-226
3
3
1.8
ENST00000265174
8
ENSE00000841650
chr4:
108578163-108578052
112
PAPS1_HUMAN
262-299
38
0
-
-
1.9
ENST00000265174
9
ENSE00000841649
chr4:
108576056-108575851
206
PAPS1_HUMAN
299-367
69
0
-
-
1.10b
ENST00000265174
10b
ENSE00001217423
chr4:
108574782-108574647
136
PAPS1_HUMAN
368-413
46
0
-
-
1.11
ENST00000265174
11
ENSE00001217417
chr4:
108566226-108565958
269
PAPS1_HUMAN
413-502
90
0
-
-
1.12a
ENST00000265174
12a
ENSE00001217412
chr4:
108553016-108552787
230
PAPS1_HUMAN
503-579
77
0
-
-
1.13
ENST00000265174
13
ENSE00001217468
chr4:
108535543-108534822
722
PAPS1_HUMAN
579-624
46
0
-
-
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2peza_ (A:)
1b: SCOP_d2pezb_ (B:)
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Protein Domains
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Organisms
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(
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Adenosine-5'phosphosulfate kinase (APS kinase)
(9)
Protein domain
:
automated matches
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2peza_
A:
1b
d2pezb_
B:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2pezA00 (A:51-226)
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
2pezA00
A:51-226
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_APS_kinase_2pezB01 (B:52-209)
1b: PFAM_APS_kinase_2pezB02 (B:52-209)
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Clan
:
P-loop_NTPase
(1112)
Family
:
APS_kinase
(10)
Homo sapiens (Human)
(7)
1a
APS_kinase-2pezB01
B:52-209
1b
APS_kinase-2pezB02
B:52-209
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Asymmetric Unit 1
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