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3H53
Asym. Unit
Info
Asym.Unit (156 KB)
Biol.Unit 1 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE
Authors
:
N. E. Clark, S. C. Garman
Date
:
21 Apr 09 (Deposition) - 20 Oct 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.01
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycoprotein, Carbohydrate-Binding Protein, Glycosidase, Lysosomal Enzyme, (Beta/Alpha)8 Barrel, Disease Mutation, Disulfide Bond, Hydrolase, Lysosome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. E. Clark, S. C. Garman
The 1. 9 A Structure Of Human Alpha-N-Acetylgalactosaminidase: The Molecular Basis Of Schindler And Kanzaki Diseases
J. Mol. Biol. V. 393 435 2009
[
close entry info
]
Hetero Components
(5, 36)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
GOL
17
Ligand/Ion
GLYCEROL
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
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
ILE A:40 , ASN A:41 , CYS A:42 , ASP A:43 , ARG A:97 , HOH A:592
BINDING SITE FOR RESIDUE GOL A 1024
02
AC2
SOFTWARE
GLN A:53 , MET A:56 , GLU A:57 , ASP A:60 , TYR A:108 , HOH A:660
BINDING SITE FOR RESIDUE GOL A 1039
03
AC3
SOFTWARE
GLY A:129 , PHE A:159
BINDING SITE FOR RESIDUE GOL A 1108
04
AC4
SOFTWARE
GLY A:129 , TYR A:130
BINDING SITE FOR RESIDUE GOL A 1113
05
AC5
SOFTWARE
THR A:25 , PRO A:26 , PRO A:27 , MET A:28 , GLY A:71 , THR A:73
BINDING SITE FOR RESIDUE GOL A 1165
06
AC6
SOFTWARE
ASP A:216 , ASP A:217 , GOL A:1201
BINDING SITE FOR RESIDUE GOL A 1200
07
AC7
SOFTWARE
MET A:128 , ASP A:217 , HOH A:538 , HOH A:829 , GOL A:1001 , GOL A:1200
BINDING SITE FOR RESIDUE GOL A 1201
08
AC8
SOFTWARE
ARG A:344 , THR A:345 , ASP A:346 , HOH A:688 , GLN B:219
BINDING SITE FOR RESIDUE GOL A 1328
09
AC9
SOFTWARE
ASN A:48 , ASP A:285 , ARG A:287 , THR A:288 , HOH A:832
BINDING SITE FOR RESIDUE GOL A 1030
10
BC1
SOFTWARE
LEU A:226 , ASN A:230 , VAL A:233 , GLU A:325 , TYR A:327 , CYS A:343 , HOH A:727
BINDING SITE FOR RESIDUE GOL A 1210
11
BC2
SOFTWARE
ASN A:124 , HOH A:581 , NAG A:625 , FUC A:627
BINDING SITE FOR RESIDUE NAG A 624
12
BC3
SOFTWARE
HOH A:581 , NAG A:624 , BMA A:626
BINDING SITE FOR RESIDUE NAG A 625
13
BC4
SOFTWARE
PHE A:159 , NAG A:625 , HOH A:809
BINDING SITE FOR RESIDUE BMA A 626
14
BC5
SOFTWARE
NAG A:624
BINDING SITE FOR RESIDUE FUC A 627
15
BC6
SOFTWARE
ASP A:19 , ASN A:20 , ASN A:177 , GLY A:180 , HOH A:498 , HOH A:596 , NAG A:678 , HOH A:774 , HOH A:775
BINDING SITE FOR RESIDUE NAG A 677
16
BC7
SOFTWARE
ASP A:19 , NAG A:677 , BMA A:679 , MAN A:681 , HOH A:804 , HOH B:725
BINDING SITE FOR RESIDUE NAG A 678
17
BC8
SOFTWARE
HOH A:512 , HOH A:604 , NAG A:678 , MAN A:680 , MAN A:681 , ARG B:61 , ASP B:65
BINDING SITE FOR RESIDUE BMA A 679
18
BC9
SOFTWARE
HOH A:616 , HOH A:622 , BMA A:679
BINDING SITE FOR RESIDUE MAN A 680
19
CC1
SOFTWARE
NAG A:678 , BMA A:679 , HOH A:728
BINDING SITE FOR RESIDUE MAN A 681
20
CC2
SOFTWARE
GLU A:383 , ASN A:385 , HOH A:425 , HOH A:472 , HOH A:542 , HOH A:595 , HOH A:719
BINDING SITE FOR RESIDUE NAG A 885
21
CC3
SOFTWARE
HOH A:12 , TRP A:33 , ASP A:78 , ASP A:79 , TYR A:119 , LYS A:154 , ASP A:156 , ARG A:213 , ASP A:217 , GOL A:1201
BINDING SITE FOR RESIDUE GOL A 1001
22
CC4
SOFTWARE
ILE B:40 , ASN B:41 , CYS B:42 , ASP B:43
BINDING SITE FOR RESIDUE GOL B 1024
23
CC5
SOFTWARE
PHE B:159
BINDING SITE FOR RESIDUE GOL B 1108
24
CC6
SOFTWARE
MET B:128 , HOH B:732
BINDING SITE FOR RESIDUE GOL B 1113
25
CC7
SOFTWARE
TYR B:192 , ASP B:216 , ASP B:217
BINDING SITE FOR RESIDUE GOL B 1200
26
CC8
SOFTWARE
ARG A:37 , GLN A:219 , ARG B:344 , THR B:345 , HOH B:644
BINDING SITE FOR RESIDUE GOL B 1328
27
CC9
SOFTWARE
ASN B:124 , HOH B:559 , NAG B:625 , FUC B:627 , HOH B:718
BINDING SITE FOR RESIDUE NAG B 624
28
DC1
SOFTWARE
HOH B:559 , NAG B:624 , FUC B:627 , HOH B:668
BINDING SITE FOR RESIDUE NAG B 625
29
DC2
SOFTWARE
NAG B:624 , NAG B:625
BINDING SITE FOR RESIDUE FUC B 627
30
DC3
SOFTWARE
ARG A:199 , ASP B:19 , ASN B:177 , GLY B:180 , HOH B:470 , HOH B:483 , HOH B:490 , HOH B:554 , NAG B:678 , HOH B:707
BINDING SITE FOR RESIDUE NAG B 677
31
DC4
SOFTWARE
ARG A:199 , ASP B:19 , GLY B:21 , NAG B:677 , BMA B:679 , MAN B:681
BINDING SITE FOR RESIDUE NAG B 678
32
DC5
SOFTWARE
NAG B:678 , MAN B:680 , MAN B:681
BINDING SITE FOR RESIDUE BMA B 679
33
DC6
SOFTWARE
BMA B:679
BINDING SITE FOR RESIDUE MAN B 680
34
DC7
SOFTWARE
NAG B:678 , BMA B:679
BINDING SITE FOR RESIDUE MAN B 681
35
DC8
SOFTWARE
GLU B:383 , ASN B:385
BINDING SITE FOR RESIDUE NAG B 885
36
DC9
SOFTWARE
ASP B:78 , ASP B:79 , TYR B:119 , LYS B:154 , ASP B:156 , ARG B:213 , ASP B:217 , HOH B:438
BINDING SITE FOR RESIDUE GOL B 1001
[
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_d3h53a2 (A:310-404)
1b: SCOP_d3h53b2 (B:310-404)
2a: SCOP_d3h53a1 (A:18-309)
2b: SCOP_d3h53b1 (B:18-309)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d3h53a2
A:310-404
1b
d3h53b2
B:310-404
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
d3h53a1
A:18-309
2b
d3h53b1
B:18-309
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3h53A01 (A:18-307)
1b: CATH_3h53B01 (B:18-307)
2a: CATH_3h53A02 (A:314-404)
2b: CATH_3h53B02 (B:314-404)
View:
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Classes
(
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(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Human (Homo sapiens)
(78)
1a
3h53A01
A:18-307
1b
3h53B01
B:18-307
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Human (Homo sapiens)
(76)
2a
3h53A02
A:314-404
2b
3h53B02
B:314-404
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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