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4DO4
Asym. Unit
Info
Asym.Unit (329 KB)
Biol.Unit 1 (320 KB)
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(1)
Title
:
PHARMACOLOGICAL CHAPERONES FOR HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE
Authors
:
N. E. Clark, S. C. Garman
Date
:
09 Feb 12 (Deposition) - 10 Oct 12 (Release) - 21 Nov 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pharmacological Chaperone, (Beta/Alpha)8 Barrel, Glycosidase, Carbohydrate-Binding Protein, Glycoprotein, Lysosome, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. E. Clark, M. C. Metcalf, D. Best, G. W. Fleet, S. C. Garman
Pharmacological Chaperones For Human Alpha-N-Acetylgalactosaminidase
Proc. Natl. Acad. Sci. Usa V. 109 17400 2012
[
close entry info
]
Hetero Components
(8, 36)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
2c: BETA-D-MANNOSE (BMAc)
3a: CITRIC ACID (CITa)
3b: CITRIC ACID (CITb)
4a: N-[(3S,4R,5S,6R)-4,5-DIHYDROXY-6-(... (DJNa)
4b: N-[(3S,4R,5S,6R)-4,5-DIHYDROXY-6-(... (DJNb)
5a: ALPHA-L-FUCOSE (FUCa)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
6i: GLYCEROL (GOLi)
6j: GLYCEROL (GOLj)
6k: GLYCEROL (GOLk)
6l: GLYCEROL (GOLl)
6m: GLYCEROL (GOLm)
7a: ALPHA-D-MANNOSE (MANa)
7b: ALPHA-D-MANNOSE (MANb)
7c: ALPHA-D-MANNOSE (MANc)
7d: ALPHA-D-MANNOSE (MANd)
8a: N-ACETYL-D-GLUCOSAMINE (NAGa)
8b: N-ACETYL-D-GLUCOSAMINE (NAGb)
8c: N-ACETYL-D-GLUCOSAMINE (NAGc)
8d: N-ACETYL-D-GLUCOSAMINE (NAGd)
8e: N-ACETYL-D-GLUCOSAMINE (NAGe)
8f: N-ACETYL-D-GLUCOSAMINE (NAGf)
8g: N-ACETYL-D-GLUCOSAMINE (NAGg)
8h: N-ACETYL-D-GLUCOSAMINE (NAGh)
8i: N-ACETYL-D-GLUCOSAMINE (NAGi)
8j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
1
Ligand/Ion
ACETIC ACID
2
BMA
3
Ligand/Ion
BETA-D-MANNOSE
3
CIT
2
Ligand/Ion
CITRIC ACID
4
DJN
2
Ligand/Ion
N-[(3S,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)PIPERIDIN-3-YL]ACETAMIDE
5
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
6
GOL
13
Ligand/Ion
GLYCEROL
7
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
8
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(36, 36)
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)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:124 , NAG A:502 , HOH A:706 , HOH A:781 , HOH A:989 , HOH A:1041
BINDING SITE FOR RESIDUE NAG A 501
02
AC2
SOFTWARE
NAG A:501 , BMA A:503
BINDING SITE FOR RESIDUE NAG A 502
03
AC3
SOFTWARE
PHE A:159 , SER A:160 , NAG A:502 , HOH A:624 , HOH A:1009 , HOH A:1033
BINDING SITE FOR RESIDUE BMA A 503
04
AC4
SOFTWARE
ASP A:19 , ASN A:20 , ASN A:177 , GLY A:180 , NAG A:505 , HOH A:643 , HOH A:728 , HOH A:812 , HOH A:892 , HOH A:1011 , HOH A:1054
BINDING SITE FOR RESIDUE NAG A 504
05
AC5
SOFTWARE
ASP A:19 , NAG A:504 , BMA A:506 , MAN A:508 , HOH A:878 , HOH A:1011
BINDING SITE FOR RESIDUE NAG A 505
06
AC6
SOFTWARE
NAG A:505 , MAN A:507 , MAN A:508 , HOH A:830 , HOH A:878 , ARG B:61 , GLN B:64 , ASP B:65
BINDING SITE FOR RESIDUE BMA A 506
07
AC7
SOFTWARE
BMA A:506
BINDING SITE FOR RESIDUE MAN A 507
08
AC8
SOFTWARE
NAG A:505 , BMA A:506 , HOH A:870
BINDING SITE FOR RESIDUE MAN A 508
09
AC9
SOFTWARE
GLU A:383 , ASN A:385 , HOH A:774 , HOH A:944
BINDING SITE FOR RESIDUE NAG A 509
10
BC1
SOFTWARE
TRP A:33 , ASP A:78 , ASP A:79 , TYR A:119 , CYS A:127 , LYS A:154 , ASP A:156 , SER A:188 , ALA A:191 , TYR A:192 , ARG A:213 , ASP A:217 , GOL A:514 , ACY A:515 , HOH A:952
BINDING SITE FOR RESIDUE DJN A 510
11
BC2
SOFTWARE
ILE A:40 , ASN A:41 , CYS A:42 , ASP A:43 , ASP A:94 , ARG A:97 , HOH A:803 , HOH A:988 , HOH A:997
BINDING SITE FOR RESIDUE CIT A 511
12
BC3
SOFTWARE
MET A:56 , GLU A:57 , ASP A:60 , TYR A:108 , HOH A:756 , HOH A:817
BINDING SITE FOR RESIDUE GOL A 512
13
BC4
SOFTWARE
GLY A:129 , HOH A:806 , HOH A:1093
BINDING SITE FOR RESIDUE GOL A 513
14
BC5
SOFTWARE
ALA A:191 , TYR A:192 , ASP A:216 , ASP A:217 , DJN A:510 , HOH A:697 , HOH A:796
BINDING SITE FOR RESIDUE GOL A 514
15
BC6
SOFTWARE
TRP A:33 , CYS A:127 , MET A:128 , DJN A:510 , HOH A:707 , HOH A:981
BINDING SITE FOR RESIDUE ACY A 515
16
BC7
SOFTWARE
ARG A:344 , THR A:345 , ASP A:346 , HOH A:1119 , GLN B:219
BINDING SITE FOR RESIDUE GOL A 516
17
BC8
SOFTWARE
LEU A:226 , LEU A:229 , ASN A:230 , VAL A:233 , GLU A:325 , TYR A:327
BINDING SITE FOR RESIDUE GOL A 517
18
BC9
SOFTWARE
PRO A:46 , SER A:51 , GLU A:52 , GLN A:53 , LYS A:96 , ARG A:97 , HOH A:1101
BINDING SITE FOR RESIDUE GOL A 518
19
CC1
SOFTWARE
ASN B:124 , PHE B:159 , SER B:160 , NAG B:502 , FUC B:503 , HOH B:1010
BINDING SITE FOR RESIDUE NAG B 501
20
CC2
SOFTWARE
NAG B:501 , FUC B:503
BINDING SITE FOR RESIDUE NAG B 502
21
CC3
SOFTWARE
NAG B:501 , NAG B:502 , HOH B:936
BINDING SITE FOR RESIDUE FUC B 503
22
CC4
SOFTWARE
ARG A:199 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , NAG B:505 , HOH B:655 , HOH B:661 , HOH B:665 , HOH B:689 , HOH B:753
BINDING SITE FOR RESIDUE NAG B 504
23
CC5
SOFTWARE
ASP B:19 , GLY B:21 , NAG B:504 , BMA B:506 , HOH B:999
BINDING SITE FOR RESIDUE NAG B 505
24
CC6
SOFTWARE
NAG B:505 , MAN B:507 , MAN B:508
BINDING SITE FOR RESIDUE BMA B 506
25
CC7
SOFTWARE
BMA B:506
BINDING SITE FOR RESIDUE MAN B 507
26
CC8
SOFTWARE
BMA B:506 , HOH B:1052
BINDING SITE FOR RESIDUE MAN B 508
27
CC9
SOFTWARE
GLU B:383 , ASN B:385 , HOH B:812 , HOH B:982
BINDING SITE FOR RESIDUE NAG B 509
28
DC1
SOFTWARE
TRP B:33 , ASP B:78 , ASP B:79 , TYR B:119 , CYS B:127 , LYS B:154 , ASP B:156 , SER B:188 , ALA B:191 , TYR B:192 , ARG B:213 , ASP B:217 , GOL B:517 , HOH B:951
BINDING SITE FOR RESIDUE DJN B 510
29
DC2
SOFTWARE
ILE B:40 , ASN B:41 , CYS B:42 , ASP B:43 , ASP B:94 , LYS B:96 , ARG B:97
BINDING SITE FOR RESIDUE CIT B 511
30
DC3
SOFTWARE
LEU B:226 , LEU B:229 , ASN B:230 , GLU B:325 , TYR B:327 , CYS B:343
BINDING SITE FOR RESIDUE GOL B 512
31
DC4
SOFTWARE
GLY B:129
BINDING SITE FOR RESIDUE GOL B 513
32
DC5
SOFTWARE
MET B:128 , TYR B:130
BINDING SITE FOR RESIDUE GOL B 514
33
DC6
SOFTWARE
TYR B:192 , ASP B:216 , ASP B:217 , HOH B:830 , HOH B:975
BINDING SITE FOR RESIDUE GOL B 515
34
DC7
SOFTWARE
ARG A:37 , GLN A:219 , ARG B:344 , THR B:345 , ASP B:346 , HOH B:922
BINDING SITE FOR RESIDUE GOL B 516
35
DC8
SOFTWARE
TRP B:33 , CYS B:127 , MET B:128 , DJN B:510 , HOH B:932
BINDING SITE FOR RESIDUE GOL B 517
36
DC9
SOFTWARE
LEU B:23 , THR B:25 , PRO B:26 , PRO B:27 , MET B:28 , THR B:73 , TYR B:74 , GLN B:307 , HOH B:744 , HOH B:791 , HOH B:933
BINDING SITE FOR RESIDUE GOL B 518
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_000496 (S160C, chain A/B, )
2: VAR_000497 (E325K, chain A/B, )
3: VAR_022525 (R329Q, chain A/B, )
4: VAR_000498 (R329W, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_000496
S
160
C
NAGAB_HUMAN
Disease (SCHIND)
121434532
A/B
S
160
C
2
UniProt
VAR_000497
E
325
K
NAGAB_HUMAN
Disease (SCHIND)
---
A/B
E
325
K
3
UniProt
VAR_022525
R
329
Q
NAGAB_HUMAN
Disease (KANZD)
121434533
A/B
R
329
Q
4
UniProt
VAR_000498
R
329
W
NAGAB_HUMAN
Disease (KANZD)
---
A/B
R
329
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ALPHA_GALACTOSIDASE (A:71-86,B:71-86)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALPHA_GALACTOSIDASE
PS00512
Alpha-galactosidase signature.
NAGAB_HUMAN
71-86
2
A:71-86
B:71-86
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4do4a2 (A:310-404)
1b: SCOP_d4do4b2 (B:310-417)
2a: SCOP_d4do4a1 (A:18-309)
2b: SCOP_d4do4b1 (B:18-309)
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Classes
(
)
(
)
Folds
(
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(
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(
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(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d4do4a2
A:310-404
1b
d4do4b2
B:310-417
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
Amylase, catalytic domain
(385)
Protein domain
:
automated matches
(71)
Human (Homo sapiens) [TaxId: 9606]
(13)
2a
d4do4a1
A:18-309
2b
d4do4b1
B:18-309
[
close SCOP info
]
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:
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Label:
Sorry, no Info available
[
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]
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Asym.Unit (329 KB)
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