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4DO6
Asym. Unit
Info
Asym.Unit (304 KB)
Biol.Unit 1 (296 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
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta/Alpha)8 Barrel, Glycosidase, Carbohydrate-Binding Protein, Glycoprotein, Lysosome, Hydrolase
(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
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Hetero Components
(8, 25)
Info
All Hetero Components
1a: NONAETHYLENE GLYCOL (2PEa)
1b: NONAETHYLENE GLYCOL (2PEb)
2a: BETA-D-GLUCOSE (BGCa)
3a: BETA-D-MANNOSE (BMAa)
3b: BETA-D-MANNOSE (BMAb)
3c: BETA-D-MANNOSE (BMAc)
4a: CITRIC ACID (CITa)
5a: ALPHA-L-FUCOSE (FUCa)
6a: ALPHA-D-GLUCOSE (GLCa)
6b: ALPHA-D-GLUCOSE (GLCb)
6c: ALPHA-D-GLUCOSE (GLCc)
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
2PE
2
Ligand/Ion
NONAETHYLENE GLYCOL
2
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
3
BMA
3
Ligand/Ion
BETA-D-MANNOSE
4
CIT
1
Ligand/Ion
CITRIC ACID
5
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
6
GLC
3
Ligand/Ion
ALPHA-D-GLUCOSE
7
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
8
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:124 , NAG A:502 , HOH A:725 , HOH A:997 , HOH A:1029
BINDING SITE FOR RESIDUE NAG A 501
02
AC2
SOFTWARE
NAG A:501 , BMA A:503 , HOH A:1040
BINDING SITE FOR RESIDUE NAG A 502
03
AC3
SOFTWARE
PHE A:159 , NAG A:502 , HOH A:855
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:639 , HOH A:735 , HOH A:825 , HOH A:870
BINDING SITE FOR RESIDUE NAG A 504
05
AC5
SOFTWARE
ASP A:19 , NAG A:504 , BMA A:506 , MAN A:508 , HOH A:889
BINDING SITE FOR RESIDUE NAG A 505
06
AC6
SOFTWARE
NAG A:505 , MAN A:507 , MAN A:508 , HOH A:889 , HOH A:1042 , GLN B:64 , ASP B:65
BINDING SITE FOR RESIDUE BMA A 506
07
AC7
SOFTWARE
BMA A:506 , HOH A:939
BINDING SITE FOR RESIDUE MAN A 507
08
AC8
SOFTWARE
NAG A:505 , BMA A:506 , HOH A:769
BINDING SITE FOR RESIDUE MAN A 508
09
AC9
SOFTWARE
GLU A:383 , ASN A:385 , HOH A:800
BINDING SITE FOR RESIDUE NAG A 509
10
BC1
SOFTWARE
ILE A:40 , ASN A:41 , CYS A:42 , ASP A:43 , ASP A:94 , LYS A:96 , ARG A:97 , HOH A:684 , HOH A:1034
BINDING SITE FOR RESIDUE CIT A 510
11
BC2
SOFTWARE
LEU A:323 , ARG A:344 , THR A:345 , ASP A:346 , HOH A:914 , ARG B:37 , GLN B:219
BINDING SITE FOR RESIDUE GLC A 511
12
BC3
SOFTWARE
GLU A:264 , ARG A:267 , ASP A:370 , SER A:373 , VAL A:395 , VAL A:396 , HOH A:620 , HOH A:751 , HOH A:1027
BINDING SITE FOR RESIDUE GLC A 512
13
BC4
SOFTWARE
ASN B:124 , PHE B:159 , SER B:160 , NAG B:502 , FUC B:503
BINDING SITE FOR RESIDUE NAG B 501
14
BC5
SOFTWARE
NAG B:501
BINDING SITE FOR RESIDUE NAG B 502
15
BC6
SOFTWARE
NAG B:501
BINDING SITE FOR RESIDUE FUC B 503
16
BC7
SOFTWARE
ARG A:199 , HOH A:727 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , NAG B:505 , HOH B:629 , HOH B:659 , HOH B:668 , HOH B:688
BINDING SITE FOR RESIDUE NAG B 504
17
BC8
SOFTWARE
ARG A:199 , ASP B:19 , GLY B:21 , NAG B:504 , BMA B:506 , MAN B:508
BINDING SITE FOR RESIDUE NAG B 505
18
BC9
SOFTWARE
NAG B:505 , MAN B:507 , MAN B:508 , HOH B:841
BINDING SITE FOR RESIDUE BMA B 506
19
CC1
SOFTWARE
BMA B:506
BINDING SITE FOR RESIDUE MAN B 507
20
CC2
SOFTWARE
NAG B:505 , BMA B:506
BINDING SITE FOR RESIDUE MAN B 508
21
CC3
SOFTWARE
GLU B:383 , ASN B:385
BINDING SITE FOR RESIDUE NAG B 509
22
CC4
SOFTWARE
ARG A:37 , GLN A:219 , LEU B:323 , ARG B:344 , THR B:345 , ASP B:346 , HOH B:720 , HOH B:921
BINDING SITE FOR RESIDUE BGC B 511
23
CC5
SOFTWARE
GLU B:264 , ARG B:267 , ASP B:370 , SER B:373 , VAL B:395 , VAL B:396 , HOH B:649 , HOH B:709 , HOH B:836
BINDING SITE FOR RESIDUE GLC B 512
[
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
[
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Exons
(0, 0)
Info
All Exons
View:
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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_d4do6a2 (A:310-405)
1b: SCOP_d4do6b2 (B:310-417)
2a: SCOP_d4do6a1 (A:18-309)
2b: SCOP_d4do6b1 (B:18-309)
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Classes
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Folds
(
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Protein Domains
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(
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Organisms
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(
)
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
d4do6a2
A:310-405
1b
d4do6b2
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
d4do6a1
A:18-309
2b
d4do6b1
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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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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