PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2Q51
Biol. Unit 1
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (102 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
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
(2, 20)
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
-1
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 only available for the asymmetric unit)
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)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
(no "Exon" information available for biological units yet)
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:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
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
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1.5 MB)
Header - Asym.Unit
Biol.Unit 1 (102 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2Q51
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
