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2Q51
Asym. Unit
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (102 KB)
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Models
(16 )
Title
:
ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF AN ASPARTOACYLASE FROM HOMO SAPIENS
Authors
:
E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date
:
31 May 07 (Deposition) - 19 Jun 07 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B (16 x)
Biol. Unit 1: A,B (1x)
Keywords
:
Ensemble Refinement, Refinement Methodology Development, Canavan Disease, N-Acetyl-L-Aspartate, Zinc-Dependent Hydrolase, Aspartoacylase Family, Aminoacylase-2, Acy2, Aspa, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 22)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
2
PO4
8
Ligand/Ion
PHOSPHATE ION
3
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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:21 , GLU A:24 , ARG A:63 , HIS A:116
BINDING SITE FOR RESIDUE ZN A 314
02
AC2
SOFTWARE
ASN A:70 , ILE A:127 , ILE A:157 , ARG A:168
BINDING SITE FOR RESIDUE PO4 A 315
03
AC3
SOFTWARE
HIS A:21 , ARG A:63 , ASP A:68 , ASN A:70 , ARG A:71 , TYR A:288
BINDING SITE FOR RESIDUE PO4 A 316
04
AC4
SOFTWARE
LYS A:103 , ASP A:104 , LYS A:163 , TYR A:164 , LYS B:163
BINDING SITE FOR RESIDUE PO4 A 317
05
AC5
SOFTWARE
ARG A:71 , HIS A:159
BINDING SITE FOR RESIDUE PO4 A 318
06
AC6
SOFTWARE
HIS B:21 , GLU B:24 , HIS B:116 , PO4 B:315
BINDING SITE FOR RESIDUE ZN B 314
07
AC7
SOFTWARE
GLU B:24 , ARG B:63 , ASN B:117 , THR B:118 , GLU B:178 , GLU B:285 , ZN B:314
BINDING SITE FOR RESIDUE PO4 B 315
08
AC8
SOFTWARE
HIS B:21 , ARG B:63 , ASP B:68 , ASN B:70 , ARG B:71 , LYS B:291
BINDING SITE FOR RESIDUE PO4 B 316
09
AC9
SOFTWARE
LYS B:103 , ASP B:104 , LYS B:163 , TYR B:164 , SER B:169 , HOH B:338
BINDING SITE FOR RESIDUE PO4 B 317
10
BC1
SOFTWARE
ARG B:71 , HIS B:159 , LYS B:228 , HOH B:329
BINDING SITE FOR RESIDUE PO4 B 318
[
close Site info
]
SAPs(SNPs)/Variants
(30, 60)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
01: VAR_039079 (I16T, chain A/B, )
02: VAR_016778 (H21P, chain A/B, )
03: VAR_016782 (E24G, chain A/B, )
04: VAR_039080 (G27R, chain A/B, )
05: VAR_016779 (A57T, chain A/B, )
06: VAR_016783 (D68A, chain A/B, )
07: VAR_039081 (D114E, chain A/B, )
08: VAR_016784 (D114Y, chain A/B, )
09: VAR_039082 (G123E, chain A/B, )
10: VAR_004995 (I143T, chain A/B, )
11: VAR_004996 (C152R, chain A/B, )
12: VAR_016785 (C152W, chain A/B, )
13: VAR_039083 (C152Y, chain A/B, )
14: VAR_039084 (R168C, chain A/B, )
15: VAR_016780 (R168H, chain A/B, )
16: VAR_016781 (P181T, chain A/B, )
17: VAR_039085 (P183H, chain A/B, )
18: VAR_039086 (V186F, chain A/B, )
19: VAR_039087 (M195R, chain A/B, )
20: VAR_016786 (Y231C, chain A/B, )
21: VAR_016787 (H244R, chain A/B, )
22: VAR_016788 (D249V, chain A/B, )
23: VAR_004998 (G274R, chain A/B, )
24: VAR_039088 (P280L, chain A/B, )
25: VAR_039089 (P280S, chain A/B, )
26: VAR_004999 (E285A, chain A/B, )
27: VAR_039090 (A287T, chain A/B, )
28: VAR_005000 (F295S, chain A/B, )
29: VAR_005001 (A305E, chain A/B, )
30: VAR_039091 (C310G, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_039079
I
16
T
ACY2_HUMAN
Disease (CAND)
---
A/B
I
16
T
02
UniProt
VAR_016778
H
21
P
ACY2_HUMAN
Disease (CAND)
---
A/B
H
21
P
03
UniProt
VAR_016782
E
24
G
ACY2_HUMAN
Disease (CAND)
---
A/B
E
24
G
04
UniProt
VAR_039080
G
27
R
ACY2_HUMAN
Disease (CAND)
---
A/B
G
27
R
05
UniProt
VAR_016779
A
57
T
ACY2_HUMAN
Disease (CAND)
---
A/B
A
57
T
06
UniProt
VAR_016783
D
68
A
ACY2_HUMAN
Disease (CAND)
---
A/B
D
68
A
07
UniProt
VAR_039081
D
114
E
ACY2_HUMAN
Disease (CAND)
---
A/B
D
114
E
08
UniProt
VAR_016784
D
114
Y
ACY2_HUMAN
Disease (CAND)
---
A/B
D
114
Y
09
UniProt
VAR_039082
G
123
E
ACY2_HUMAN
Disease (CAND)
---
A/B
G
123
E
10
UniProt
VAR_004995
I
143
T
ACY2_HUMAN
Disease (CAND)
---
A/B
I
143
T
11
UniProt
VAR_004996
C
152
R
ACY2_HUMAN
Disease (CAND)
---
A/B
C
152
R
12
UniProt
VAR_016785
C
152
W
ACY2_HUMAN
Disease (CAND)
---
A/B
C
152
W
13
UniProt
VAR_039083
C
152
Y
ACY2_HUMAN
Disease (CAND)
---
A/B
C
152
Y
14
UniProt
VAR_039084
R
168
C
ACY2_HUMAN
Disease (CAND)
---
A/B
R
168
C
15
UniProt
VAR_016780
R
168
H
ACY2_HUMAN
Disease (CAND)
---
A/B
R
168
H
16
UniProt
VAR_016781
P
181
T
ACY2_HUMAN
Disease (CAND)
---
A/B
P
181
T
17
UniProt
VAR_039085
P
183
H
ACY2_HUMAN
Disease (CAND)
---
A/B
P
183
H
18
UniProt
VAR_039086
V
186
F
ACY2_HUMAN
Disease (CAND)
---
A/B
V
186
F
19
UniProt
VAR_039087
M
195
R
ACY2_HUMAN
Disease (CAND)
---
A/B
M
195
R
20
UniProt
VAR_016786
Y
231
C
ACY2_HUMAN
Disease (CAND)
---
A/B
Y
231
C
21
UniProt
VAR_016787
H
244
R
ACY2_HUMAN
Disease (CAND)
---
A/B
H
244
R
22
UniProt
VAR_016788
D
249
V
ACY2_HUMAN
Disease (CAND)
---
A/B
D
249
V
23
UniProt
VAR_004998
G
274
R
ACY2_HUMAN
Disease (CAND)
---
A/B
G
274
R
24
UniProt
VAR_039088
P
280
L
ACY2_HUMAN
Disease (CAND)
---
A/B
P
280
L
25
UniProt
VAR_039089
P
280
S
ACY2_HUMAN
Disease (CAND)
---
A/B
P
280
S
26
UniProt
VAR_004999
E
285
A
ACY2_HUMAN
Disease (CAND)
28940279
A/B
E
285
A
27
UniProt
VAR_039090
A
287
T
ACY2_HUMAN
Disease (CAND)
---
A/B
A
287
T
28
UniProt
VAR_005000
F
295
S
ACY2_HUMAN
Disease (CAND)
---
A/B
F
295
S
29
UniProt
VAR_005001
A
305
E
ACY2_HUMAN
Disease (CAND)
28940574
A/B
A
305
E
30
UniProt
VAR_039091
C
310
G
ACY2_HUMAN
Polymorphism
---
A/B
C
310
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.2a (A:9-79 | B:9-79)
Exon 1.3 (A:79-144 | B:79-144)
Exon 1.4 (A:145-176 | B:145-176)
Exon 1.5 (A:176-212 | B:176-212)
Exon 1.6 (A:212-248 | B:212-248)
Exon 1.7b (A:249-310 | B:249-310)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7b
7: Boundary 1.7b/-
View:
Label:
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
1.2a
ENST00000263080
2a
ENSE00001116147
chr17:
3379296-3379689
394
ACY2_HUMAN
1-79
79
2
A:9-79
B:9-79
71
71
1.3
ENST00000263080
3
ENSE00000669162
chr17:
3384897-3385092
196
ACY2_HUMAN
79-144
66
2
A:79-144
B:79-144
66
66
1.4
ENST00000263080
4
ENSE00000669164
chr17:
3386793-3386886
94
ACY2_HUMAN
145-176
32
2
A:145-176
B:145-176
32
32
1.5
ENST00000263080
5
ENSE00000669166
chr17:
3392529-3392636
108
ACY2_HUMAN
176-212
37
2
A:176-212
B:176-212
37
37
1.6
ENST00000263080
6
ENSE00000669168
chr17:
3397644-3397753
110
ACY2_HUMAN
212-248
37
2
A:212-248
B:212-248
37
37
1.7b
ENST00000263080
7b
ENSE00001923034
chr17:
3402185-3406713
4529
ACY2_HUMAN
249-313
65
2
A:249-310
B:249-310
62
62
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2q51a_ (A:)
1b: SCOP_d2q51b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
AstE/AspA-like
(10)
Protein domain
:
Aspartoacylase AspA
(5)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d2q51a_
A:
1b
d2q51b_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_AstE_AspA_2q51B01 (B:10-301)
1b: PFAM_AstE_AspA_2q51B02 (B:10-301)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MH
(119)
Family
:
AstE_AspA
(12)
Homo sapiens (Human)
(2)
1a
AstE_AspA-2q51B01
B:10-301
1b
AstE_AspA-2q51B02
B:10-301
[
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]
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Nucleic
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Protein & NOT PROSITE
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Asymmetric Unit 1
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