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4BVH
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (52 KB)
Biol.Unit 2 (52 KB)
Biol.Unit 3 (52 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE
Authors
:
M. Gertz, M. Weyand, C. Steegborn
Date
:
25 Jun 13 (Deposition) - 17 Jul 13 (Release) - 07 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Hydrolase, Inhibitor Complex, Ex-527
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Gertz, F. Fischer, G. T. T. Nguyen, M. Lakshminarasimhan, M. Schutkowski, M. Weyand, C. Steegborn
Ex-527 Inhibits Sirtuins By Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism
Proc. Natl. Acad. Sci. Usa V. 110 E2772 2013
[
close entry info
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Hetero Components
(8, 18)
Info
All Hetero Components
1a: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-Y... (AR6a)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
4a: GLYCEROL (GOLa)
5a: SODIUM ION (NAa)
6a: 2'-O-ACETYL ADENOSINE-5-DIPHOSPHOR... (OADa)
6b: 2'-O-ACETYL ADENOSINE-5-DIPHOSPHOR... (OADb)
7a: (1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1... (OCZa)
7b: (1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1... (OCZb)
7c: (1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1... (OCZc)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
8c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AR6
1
Ligand/Ion
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
4
GOL
1
Ligand/Ion
GLYCEROL
5
NA
1
Ligand/Ion
SODIUM ION
6
OAD
2
Ligand/Ion
2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
7
OCZ
3
Ligand/Ion
(1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-1- CARBOXAMIDE
8
ZN
3
Ligand/Ion
ZINC ION
[
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Sites
(17, 17)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:155 , PHE A:157 , PHE A:180 , GLN A:228 , ASN A:229 , ILE A:230 , ASP A:231 , HIS A:248 , ILE A:291 , PHE A:293 , OAD A:1394 , HOH A:2018 , HOH A:2019
BINDING SITE FOR RESIDUE OCZ A1393
02
AC2
SOFTWARE
GLY A:145 , ALA A:146 , GLY A:147 , THR A:150 , ASP A:156 , PHE A:157 , ARG A:158 , TYR A:165 , PHE A:180 , GLN A:228 , HIS A:248 , PHE A:294 , GLY A:319 , THR A:320 , SER A:321 , VAL A:324 , ASN A:344 , ARG A:345 , GLY A:364 , ASP A:365 , VAL A:366 , OCZ A:1393 , HOH A:2018 , HOH A:2105
BINDING SITE FOR RESIDUE OAD A1394
03
AC3
SOFTWARE
CYS A:256 , CYS A:259 , CYS A:280 , CYS A:283
BINDING SITE FOR RESIDUE ZN A1395
04
AC4
SOFTWARE
ASP A:172 , HIS A:187 , HIS C:354
BINDING SITE FOR RESIDUE NA A1396
05
AC5
SOFTWARE
GLN A:138 , LEU A:222
BINDING SITE FOR RESIDUE CL A1397
06
AC6
SOFTWARE
PHE B:157 , PHE B:180 , GLN B:228 , ASN B:229 , ILE B:230 , ASP B:231 , HIS B:248 , ILE B:291 , AR6 B:1393 , HOH B:2010 , HOH B:2011
BINDING SITE FOR RESIDUE OCZ B1392
07
AC7
SOFTWARE
GLY B:145 , ALA B:146 , GLY B:147 , THR B:150 , ASP B:156 , PHE B:157 , ARG B:158 , TYR B:165 , GLN B:228 , HIS B:248 , PHE B:294 , GLY B:319 , THR B:320 , SER B:321 , VAL B:324 , ASN B:344 , ARG B:345 , GLY B:364 , ASP B:365 , VAL B:366 , OCZ B:1392 , HOH B:2010 , HOH B:2131
BINDING SITE FOR RESIDUE AR6 B1393
08
AC8
SOFTWARE
PRO B:310 , ALA B:312 , ARG B:335 , LYS C:190 , THR C:194
BINDING SITE FOR RESIDUE EDO B1394
09
AC9
SOFTWARE
ASP A:127 , LEU A:131 , VAL B:236 , HOH B:2062 , HOH B:2082
BINDING SITE FOR RESIDUE EDO B1395
10
BC1
SOFTWARE
CYS B:256 , VAL B:258 , CYS B:259 , CYS B:280 , CYS B:283
BINDING SITE FOR RESIDUE ZN B1396
11
BC2
SOFTWARE
ILE C:154 , PRO C:155 , PHE C:157 , PHE C:180 , GLN C:228 , ASN C:229 , ILE C:230 , ASP C:231 , HIS C:248 , ILE C:291 , VAL C:292 , OAD C:1395 , HOH C:2018
BINDING SITE FOR RESIDUE OCZ C1394
12
BC3
SOFTWARE
GLY C:145 , ALA C:146 , GLY C:147 , THR C:150 , ASP C:156 , PHE C:157 , ARG C:158 , SER C:159 , TYR C:165 , GLN C:228 , HIS C:248 , VAL C:292 , PHE C:294 , GLY C:319 , THR C:320 , SER C:321 , VAL C:324 , ASN C:344 , ARG C:345 , GLY C:364 , ASP C:365 , VAL C:366 , OCZ C:1394 , HOH C:2017 , HOH C:2143 , HOH C:2197
BINDING SITE FOR RESIDUE OAD C1395
13
BC4
SOFTWARE
LEU C:131 , ARG C:358 , THR C:391 , HOH C:2142
BINDING SITE FOR RESIDUE EDO C1396
14
BC5
SOFTWARE
ASP C:267 , GLU C:382 , ASP C:385 , HOH C:2193 , HOH C:2196
BINDING SITE FOR RESIDUE GOL C1397
15
BC6
SOFTWARE
THR B:150 , GLY B:153 , GLN C:300 , ARG C:301 , LEU C:304 , HOH C:2138
BINDING SITE FOR RESIDUE EDO C1398
16
BC7
SOFTWARE
LYS C:122 , ASP C:359
BINDING SITE FOR RESIDUE EDO C1399
17
BC8
SOFTWARE
CYS C:256 , CYS C:259 , CYS C:280 , CYS C:283
BINDING SITE FOR RESIDUE ZN C1400
[
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SAPs(SNPs)/Variants
(2, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_051978 (V208I, chain A/B/C, )
2: VAR_051979 (G369S, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051978
V
208
I
SIR3_HUMAN
Polymorphism
11246020
A/B/C
V
208
I
2
UniProt
VAR_051979
G
369
S
SIR3_HUMAN
Polymorphism
3020901
A/B/C
G
369
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: SIRTUIN (A:126-382,B:126-382,C:126-382)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SIRTUIN
PS50305
Sirtuin catalytic domain profile.
SIR3_HUMAN
126-382
3
A:126-382
B:126-382
C:126-382
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d4bvha_ (A:)
1b: SCOP_d4bvhb_ (B:)
1c: SCOP_d4bvhc_ (C:)
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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
:
automated matches
(36)
Protein domain
:
automated matches
(36)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d4bvha_
A:
1b
d4bvhb_
B:
1c
d4bvhc_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Chain C
Asymmetric Unit 1
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Asym.Unit (154 KB)
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