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4BM9
Biol. Unit 1
Info
Asym.Unit (107 KB)
Biol.Unit 1 (589 KB)
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(1)
Title
:
STRUCTURE OF THE AUTOINHIBITED PARKIN CATALYTIC DOMAIN
Authors
:
T. Wauer, D. Komander
Date
:
07 May 13 (Deposition) - 12 Jun 13 (Release) - 14 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A
Biol. Unit 1: A (6x)
Keywords
:
Ligase, Neurodegenerative Disease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Wauer, D. Komander
Structure Of The Human Parkin Ligase Domain In An Autoinhibited State.
Embo J. V. 32 2099 2013
[
close entry info
]
Hetero Components
(2, 24)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
6
Ligand/Ion
GLYCEROL
2
SO4
18
Ligand/Ion
SULFATE ION
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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:150 , CYS A:154 , CYS A:212 , HIS A:215
BINDING SITE FOR RESIDUE ZN A1466
02
AC2
SOFTWARE
CYS A:253 , HIS A:257 , CYS A:289 , CYS A:293
BINDING SITE FOR RESIDUE ZN A1467
03
AC3
SOFTWARE
CYS A:446 , CYS A:449 , CYS A:457 , HIS A:461
BINDING SITE FOR RESIDUE ZN A1468
04
AC4
SOFTWARE
CYS A:166 , CYS A:169 , CYS A:196 , CYS A:201
BINDING SITE FOR RESIDUE ZN A1469
05
AC5
SOFTWARE
CYS A:238 , CYS A:241 , CYS A:260 , CYS A:263
BINDING SITE FOR RESIDUE ZN A1470
06
AC6
SOFTWARE
CYS A:332 , CYS A:337 , CYS A:352
BINDING SITE FOR RESIDUE ZN A1471
07
AC7
SOFTWARE
CYS A:365 , CYS A:368 , HIS A:373 , CYS A:377
BINDING SITE FOR RESIDUE ZN A1472
08
AC8
SOFTWARE
CYS A:418 , CYS A:421 , CYS A:436 , CYS A:441
BINDING SITE FOR RESIDUE ZN A1473
09
AC9
SOFTWARE
ARG A:163 , LYS A:211 , ARG A:420 , HOH A:2045
BINDING SITE FOR RESIDUE SO4 A1474
10
BC1
SOFTWARE
ASN A:454 , ARG A:455
BINDING SITE FOR RESIDUE SO4 A1475
11
BC2
SOFTWARE
LYS A:151 , HIS A:302 , ARG A:305 , TYR A:312 , HOH A:2087
BINDING SITE FOR RESIDUE SO4 A1476
12
BC3
SOFTWARE
LYS A:416 , TRP A:447 , ASN A:448
BINDING SITE FOR RESIDUE GOL A1477
[
close Site info
]
SAPs(SNPs)/Variants
(32, 192)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_019741 (K161N, chain A, )
02: VAR_019742 (S167N, chain A, )
03: VAR_054107 (M192L, chain A, )
04: VAR_019743 (M192V, chain A, )
05: VAR_019744 (K211N, chain A, )
06: VAR_019745 (K211R, chain A, )
07: VAR_019746 (C212Y, chain A, )
08: VAR_019747 (T240M, chain A, )
09: VAR_019748 (T240R, chain A, )
10: VAR_019749 (C253Y, chain A, )
11: VAR_019750 (R256C, chain A, )
12: VAR_019751 (R271S, chain A, )
13: VAR_019752 (R275W, chain A, )
14: VAR_019753 (D280N, chain A, )
15: VAR_019754 (G284R, chain A, )
16: VAR_019755 (C289G, chain A, )
17: VAR_062672 (Q311R, chain A, )
18: VAR_019756 (G328E, chain A, )
19: VAR_019757 (R334C, chain A, )
20: VAR_019758 (A339S, chain A, )
21: VAR_019759 (T351P, chain A, )
22: VAR_019760 (R366W, chain A, )
23: VAR_062673 (A371T, chain A, )
24: VAR_019761 (V380L, chain A, )
25: VAR_019762 (D394N, chain A, )
26: VAR_070079 (R402C, chain A, )
27: VAR_019763 (T415N, chain A, )
28: VAR_070080 (C418R, chain A, )
29: VAR_019764 (G430D, chain A, )
30: VAR_019765 (C431F, chain A, )
31: VAR_019766 (P437L, chain A, )
32: VAR_019767 (C441R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_019741
K
161
N
PRKN2_HUMAN
Disease (PARK2)
---
A
K
161
N
02
UniProt
VAR_019742
S
167
N
PRKN2_HUMAN
Polymorphism
1801474
A
S
167
N
03
UniProt
VAR_054107
M
192
L
PRKN2_HUMAN
Unclassified
9456735
A
M
192
L
04
UniProt
VAR_019743
M
192
V
PRKN2_HUMAN
Unclassified
9456735
A
M
192
V
05
UniProt
VAR_019744
K
211
N
PRKN2_HUMAN
Disease (PARK2)
---
A
K
211
N
06
UniProt
VAR_019745
K
211
R
PRKN2_HUMAN
Disease (PARK2)
---
A
K
211
R
07
UniProt
VAR_019746
C
212
Y
PRKN2_HUMAN
Disease (PARK2)
---
A
C
212
Y
08
UniProt
VAR_019747
T
240
M
PRKN2_HUMAN
Disease (PARK2)
---
A
T
240
M
09
UniProt
VAR_019748
T
240
R
PRKN2_HUMAN
Disease (PARK2)
---
A
T
240
R
10
UniProt
VAR_019749
C
253
Y
PRKN2_HUMAN
Disease (PARK)
---
A
C
253
Y
11
UniProt
VAR_019750
R
256
C
PRKN2_HUMAN
Disease (PARK)
150562946
A
R
256
C
12
UniProt
VAR_019751
R
271
S
PRKN2_HUMAN
Polymorphism
---
A
R
271
S
13
UniProt
VAR_019752
R
275
W
PRKN2_HUMAN
Disease (PARK)
34424986
A
R
275
W
14
UniProt
VAR_019753
D
280
N
PRKN2_HUMAN
Disease (PARK)
---
A
D
280
N
15
UniProt
VAR_019754
G
284
R
PRKN2_HUMAN
Disease (PARK2)
---
A
G
284
R
16
UniProt
VAR_019755
C
289
G
PRKN2_HUMAN
Disease (PARK2)
55961220
A
C
289
G
17
UniProt
VAR_062672
Q
311
R
PRKN2_HUMAN
Unclassified
---
A
Q
311
R
18
UniProt
VAR_019756
G
328
E
PRKN2_HUMAN
Disease (PARK2)
---
A
G
328
E
19
UniProt
VAR_019757
R
334
C
PRKN2_HUMAN
Disease (PARK2)
---
A
R
334
C
20
UniProt
VAR_019758
A
339
S
PRKN2_HUMAN
Polymorphism
---
A
A
339
S
21
UniProt
VAR_019759
T
351
P
PRKN2_HUMAN
Disease (PARK2)
---
A
T
351
P
22
UniProt
VAR_019760
R
366
W
PRKN2_HUMAN
Polymorphism
56092260
A
R
366
W
23
UniProt
VAR_062673
A
371
T
PRKN2_HUMAN
Unclassified
---
A
A
371
T
24
UniProt
VAR_019761
V
380
L
PRKN2_HUMAN
Polymorphism
1801582
A
V
380
L
25
UniProt
VAR_019762
D
394
N
PRKN2_HUMAN
Polymorphism
1801334
A
D
394
N
26
UniProt
VAR_070079
R
402
C
PRKN2_HUMAN
Disease (PARK2)
---
A
R
402
C
27
UniProt
VAR_019763
T
415
N
PRKN2_HUMAN
Disease (PARK2)
---
A
T
415
N
28
UniProt
VAR_070080
C
418
R
PRKN2_HUMAN
Disease (PARK2)
---
A
C
418
R
29
UniProt
VAR_019764
G
430
D
PRKN2_HUMAN
Disease (PARK2)
---
A
G
430
D
30
UniProt
VAR_019765
C
431
F
PRKN2_HUMAN
Disease (PARK2)
---
A
C
431
F
31
UniProt
VAR_019766
P
437
L
PRKN2_HUMAN
Disease (PARK2)
149953814
A
P
437
L
32
UniProt
VAR_019767
C
441
R
PRKN2_HUMAN
Disease (PARK2)
---
A
C
441
R
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
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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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
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
Asymmetric Unit 5
Asymmetric Unit 6
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