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1Q17
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (149 KB)
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(1)
Title
:
STRUCTURE OF THE YEAST HST2 PROTEIN DEACETYLASE IN TERNARY COMPLEX WITH 2'-O-ACETYL ADP RIBOSE AND HISTONE PEPTIDE
Authors
:
K. Zhao, X. Chai, R. Marmorstein
Date
:
18 Jul 03 (Deposition) - 18 Nov 03 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Histone Deacetylase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Zhao, X. Chai, R. Marmorstein
Structure Of The Yeast Hst2 Protein Deacetylase In Ternary Complex With 2'-O-Acetyl Adp Ribose And Histone Peptide.
Structure V. 11 1403 2003
(for further references see the
PDB file header
)
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: ADENOSINE-5-DIPHOSPHORIBOSE (APRa)
1b: ADENOSINE-5-DIPHOSPHORIBOSE (APRb)
1c: ADENOSINE-5-DIPHOSPHORIBOSE (APRc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APR
3
Ligand/Ion
ADENOSINE-5-DIPHOSPHORIBOSE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
ZN
3
Ligand/Ion
ZINC 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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:143 , CYS A:146 , CYS A:170 , CYS A:173
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
CYS B:143 , CYS B:146 , CYS B:170 , CYS B:173
BINDING SITE FOR RESIDUE ZN B 401
03
AC3
SOFTWARE
CYS C:143 , CYS C:146 , CYS C:170 , CYS C:173
BINDING SITE FOR RESIDUE ZN C 401
04
AC4
SOFTWARE
ARG C:204 , ARG C:240
BINDING SITE FOR RESIDUE CL C 701
05
AC5
SOFTWARE
TRP B:202
BINDING SITE FOR RESIDUE CL B 702
06
AC6
SOFTWARE
ARG A:204 , ARG A:240
BINDING SITE FOR RESIDUE CL A 703
07
AC7
SOFTWARE
ARG B:204 , ARG B:240
BINDING SITE FOR RESIDUE CL B 704
08
AC8
SOFTWARE
GLY A:32 , ALA A:33 , GLY A:34 , THR A:37 , ASP A:43 , PHE A:44 , ARG A:45 , TYR A:52 , GLN A:115 , HIS A:135 , GLY A:223 , THR A:224 , SER A:225 , VAL A:228 , ASN A:248 , LEU A:249 , GLU A:250 , GLN A:268 , TYR A:269 , SER A:270 , HOH A:1003 , HOH A:1025 , HOH A:1041
BINDING SITE FOR RESIDUE APR A 1001
09
AC9
SOFTWARE
GLY B:32 , ALA B:33 , GLY B:34 , THR B:37 , ASP B:43 , PHE B:44 , ARG B:45 , TYR B:52 , GLN B:115 , HIS B:135 , GLY B:223 , THR B:224 , SER B:225 , VAL B:228 , ASN B:248 , LEU B:249 , GLN B:268 , TYR B:269 , SER B:270 , HOH B:1007 , HOH B:1009 , HOH B:1023 , HOH B:1024 , HOH B:1046
BINDING SITE FOR RESIDUE APR B 1002
10
BC1
SOFTWARE
GLY C:32 , ALA C:33 , GLY C:34 , THR C:37 , ASP C:43 , PHE C:44 , ARG C:45 , TYR C:52 , GLN C:115 , HIS C:135 , GLY C:223 , THR C:224 , SER C:225 , VAL C:228 , ASN C:248 , LEU C:249 , GLN C:268 , TYR C:269 , SER C:270 , HOH C:1022
BINDING SITE FOR RESIDUE APR C 1003
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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
(1, 3)
Info
All PROSITE Patterns/Profiles
1: SIRTUIN (A:13-286,B:13-286,C:13-286)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SIRTUIN
PS50305
Sirtuin catalytic domain profile.
HST2_YEAST
13-286
3
A:13-286
B:13-286
C:13-286
[
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Exons
(1, 3)
Info
All Exons
Exon 1.1 (A:1-294 (gaps) | B:1-294 (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
YPL015C
1
YPL015C.1
XVI:526880-525807
1074
HST2_YEAST
1-357
357
3
A:1-294 (gaps)
B:1-294 (gaps)
C:1-294 (gaps)
294
294
294
[
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]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1q17a_ (A:)
1b: SCOP_d1q17b_ (B:)
1c: SCOP_d1q17c_ (C:)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
Sir2 family of transcriptional regulators
(31)
Protein domain
:
Hst2
(5)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
1a
d1q17a_
A:
1b
d1q17b_
B:
1c
d1q17c_
C:
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1q17A02 (A:38-93,A:135-189)
1b: CATH_1q17B02 (B:38-93,B:135-189)
1c: CATH_1q17C02 (C:38-93,C:135-189)
2a: CATH_1q17A01 (A:-3-37,A:94-134,A:190-294)
2b: CATH_1q17B01 (B:-3-37,B:94-134,B:190-294)
2c: CATH_1q17C01 (C:-3-37,C:94-134,C:190-294)
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Topologies
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Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
SIR2/SIRT2 'Small Domain'
(25)
Homologous Superfamily
:
SIR2/SIRT2 'Small Domain'
(25)
Baker's yeast (Saccharomyces cerevisiae)
(10)
1a
1q17A02
A:38-93,A:135-189
1b
1q17B02
B:38-93,B:135-189
1c
1q17C02
C:38-93,C:135-189
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
TPP-binding domain
(120)
Baker's yeast (Saccharomyces cerevisiae)
(20)
2a
1q17A01
A:-3-37,A:94-134,A:190-294
2b
1q17B01
B:-3-37,B:94-134,B:190-294
2c
1q17C01
C:-3-37,C:94-134,C:190-294
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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