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2B4Y
Asym. Unit
Info
Asym.Unit (188 KB)
Biol.Unit 1 (49 KB)
Biol.Unit 2 (49 KB)
Biol.Unit 3 (49 KB)
Biol.Unit 4 (48 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN SIRTUIN HOMOLOG 5
Authors
:
J. R. Min, T. Antoshenko, A. Dong, A. Schuetz, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date
:
27 Sep 05 (Deposition) - 28 Feb 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Histone Deacetylase, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Antoshenko, J. R. Min, A. Schuetz, P. Loppnau, A. M. Edwards, C. H. Arrowsmith, A. Bochkarev, A. N. Plotnikov
Crystal Structure Of Human Sirtuin Homolog 5 In Complex With Nad
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 24)
Info
All Hetero Components
1a: ADENOSINE-5-DIPHOSPHORIBOSE (APRa)
1b: ADENOSINE-5-DIPHOSPHORIBOSE (APRb)
1c: ADENOSINE-5-DIPHOSPHORIBOSE (APRc)
1d: ADENOSINE-5-DIPHOSPHORIBOSE (APRd)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APR
4
Ligand/Ion
ADENOSINE-5-DIPHOSPHORIBOSE
2
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
4
ZN
4
Ligand/Ion
ZINC ION
[
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]
Sites
(12, 12)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:166 , CYS A:169 , CYS A:207 , CYS A:212
BINDING SITE FOR RESIDUE ZN A 1001
02
AC2
SOFTWARE
CYS B:166 , CYS B:169 , CYS B:207 , CYS B:212
BINDING SITE FOR RESIDUE ZN B 2001
03
AC3
SOFTWARE
CYS C:166 , CYS C:169 , CYS C:207 , CYS C:212
BINDING SITE FOR RESIDUE ZN C 3001
04
AC4
SOFTWARE
CYS D:166 , CYS D:169 , CYS D:207 , CYS D:212
BINDING SITE FOR RESIDUE ZN D 4001
05
AC5
SOFTWARE
GLY A:58 , ALA A:59 , GLY A:60 , ALA A:63 , GLU A:64 , GLN A:140 , HIS A:158 , GLY A:249 , THR A:250 , SER A:251 , ASN A:275 , THR A:276 , GLU A:277 , PRO A:292 , CYS A:293 , EPE A:1003 , HOH A:1033 , HOH A:1070 , HOH A:1160 , HOH A:1176 , HOH A:1190
BINDING SITE FOR RESIDUE APR A 1002
06
AC6
SOFTWARE
GLY B:58 , ALA B:59 , GLY B:60 , GLU B:64 , THR B:69 , GLN B:140 , HIS B:158 , GLY B:249 , THR B:250 , SER B:251 , ASN B:275 , THR B:276 , GLU B:277 , CYS B:293 , EPE B:2003 , HOH B:2028 , HOH B:2031 , HOH B:2160 , HOH B:2171
BINDING SITE FOR RESIDUE APR B 2002
07
AC7
SOFTWARE
HOH B:2043 , GLY C:58 , ALA C:59 , GLY C:60 , ALA C:63 , GLU C:64 , THR C:69 , PHE C:70 , ARG C:71 , GLN C:140 , HIS C:158 , GLY C:249 , THR C:250 , SER C:251 , VAL C:254 , ASN C:275 , THR C:276 , GLU C:277 , PRO C:292 , CYS C:293 , EPE C:3003 , HOH C:3005 , HOH C:3067 , HOH C:3082 , HOH C:3145
BINDING SITE FOR RESIDUE APR C 3002
08
AC8
SOFTWARE
GLY D:58 , ALA D:59 , GLY D:60 , GLU D:64 , THR D:69 , PHE D:70 , GLN D:140 , HIS D:158 , GLY D:249 , THR D:250 , SER D:251 , VAL D:254 , ASN D:275 , THR D:276 , GLU D:277 , PRO D:292 , CYS D:293 , EPE D:4003 , HOH D:4007 , HOH D:4039 , HOH D:4072 , HOH D:4128 , HOH D:4135
BINDING SITE FOR RESIDUE APR D 4002
09
AC9
SOFTWARE
ALA A:82 , ALA A:86 , TYR A:102 , ARG A:105 , HIS A:158 , VAL A:221 , TRP A:222 , PHE A:223 , GLY A:224 , GLU A:225 , APR A:1002 , HOH A:1186
BINDING SITE FOR RESIDUE EPE A 1003
10
BC1
SOFTWARE
ALA B:82 , ALA B:86 , TYR B:102 , ARG B:105 , VAL B:221 , TRP B:222 , PHE B:223 , APR B:2002
BINDING SITE FOR RESIDUE EPE B 2003
11
BC2
SOFTWARE
PHE C:70 , ALA C:82 , ALA C:86 , ARG C:105 , HIS C:158 , VAL C:221 , PHE C:223 , GLU C:225 , LEU C:227 , APR C:3002 , HOH C:3144 , HOH C:3147 , SER D:168 , CYS D:169
BINDING SITE FOR RESIDUE EPE C 3003
12
BC3
SOFTWARE
SER C:168 , CYS C:169 , PHE D:70 , ALA D:82 , ALA D:86 , ARG D:105 , HIS D:158 , VAL D:221 , PHE D:223 , GLU D:225 , LEU D:227 , TYR D:255 , APR D:4002 , HOH D:4125 , HOH D:4149
BINDING SITE FOR RESIDUE EPE D 4003
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_029042 (F285L, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_029042
F
285
L
SIR5_HUMAN
Polymorphism
9464003
A/B/C/D
F
285
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: SIRTUIN (A:41-302,B:41-302,C:41-302,D:41-30...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SIRTUIN
PS50305
Sirtuin catalytic domain profile.
SIR5_HUMAN
41-309
4
A:41-302
B:41-302
C:41-302
D:41-302
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2b4ya1 (A:36-302)
1b: SCOP_d2b4yb_ (B:)
1c: SCOP_d2b4yc_ (C:)
1d: SCOP_d2b4yd_ (D:)
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(
)
(
)
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
:
NAD-dependent deacetylase sirtuin-5
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2b4ya1
A:36-302
1b
d2b4yb_
B:
1c
d2b4yc_
C:
1d
d2b4yd_
D:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2b4yB01 (B:36-66,B:114-158,B:227-302)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
TPP-binding domain
(120)
Human (Homo sapiens)
(9)
1a
2b4yB01
B:36-66,B:114-158,B:227-302
[
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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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