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3H55
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX WITH GALACTOSE
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
:
1.91
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycoprotein, Carbohydrate-Binding Protein, Glycosidase, Lysosomal Enzyme, (Beta/Alpha)8 Barrel, Protein-Ligand Complex, 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
(6, 25)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: CITRIC ACID (CITa)
2b: CITRIC ACID (CITb)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: ALPHA D-GALACTOSE (GLAa)
4b: ALPHA D-GALACTOSE (GLAb)
4c: ALPHA D-GALACTOSE (GLAc)
4d: ALPHA D-GALACTOSE (GLAd)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
5d: ALPHA-D-MANNOSE (MANd)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
CIT
2
Ligand/Ion
CITRIC ACID
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GLA
4
Ligand/Ion
ALPHA D-GALACTOSE
5
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:124 , PHE A:159 , HOH A:531 , NAG A:625 , BMA A:626 , FUC A:627 , HOH A:629 , HOH A:753 , HOH A:851
BINDING SITE FOR RESIDUE NAG A 624
02
AC2
SOFTWARE
NAG A:624 , BMA A:626 , HOH A:715
BINDING SITE FOR RESIDUE NAG A 625
03
AC3
SOFTWARE
PHE A:159 , NAG A:624 , NAG A:625
BINDING SITE FOR RESIDUE BMA A 626
04
AC4
SOFTWARE
NAG A:624 , HOH A:788 , HOH A:816 , HOH A:851
BINDING SITE FOR RESIDUE FUC A 627
05
AC5
SOFTWARE
ASP A:19 , ASN A:20 , ASN A:177 , GLY A:180 , ARG A:181 , HOH A:492 , HOH A:542 , NAG A:678 , HOH A:793 , HOH A:810 , HOH A:811
BINDING SITE FOR RESIDUE NAG A 677
06
AC6
SOFTWARE
ASP A:19 , HOH A:532 , HOH A:569 , NAG A:677 , BMA A:679 , MAN A:681 , HOH A:849 , HOH A:869
BINDING SITE FOR RESIDUE NAG A 678
07
AC7
SOFTWARE
HOH A:483 , NAG A:678 , MAN A:680 , MAN A:681 , ARG B:61 , GLN B:64 , ASP B:65
BINDING SITE FOR RESIDUE BMA A 679
08
AC8
SOFTWARE
HOH A:559 , BMA A:679
BINDING SITE FOR RESIDUE MAN A 680
09
AC9
SOFTWARE
HOH A:589 , HOH A:595 , NAG A:678 , BMA A:679
BINDING SITE FOR RESIDUE MAN A 681
10
BC1
SOFTWARE
GLU A:383 , ASN A:385 , HOH A:541 , HOH A:735 , HOH A:908
BINDING SITE FOR RESIDUE NAG A 885
11
BC2
SOFTWARE
HOH A:12 , TRP A:33 , ASP A:78 , ASP A:79 , TYR A:119 , CYS A:127 , MET A:128 , LYS A:154 , ASP A:156 , ARG A:213 , ASP A:217 , HOH A:686 , HOH A:893 , HOH A:895 , GLA A:1500
BINDING SITE FOR RESIDUE GLA A 1000
12
BC3
SOFTWARE
ALA A:191 , TYR A:192 , TYR A:215 , ASP A:217 , HOH A:686 , HOH A:733 , HOH A:791 , GLA A:1000
BINDING SITE FOR RESIDUE GLA A 1500
13
BC4
SOFTWARE
HIS A:110 , GLY A:113 , LEU A:114 , LYS A:115 , ASP A:151 , ARG A:181 , HOH A:425 , HOH A:444 , HOH A:580 , HOH A:685
BINDING SITE FOR RESIDUE CIT A 1100
14
BC5
SOFTWARE
ASN B:124 , NAG B:625 , FUC B:627
BINDING SITE FOR RESIDUE NAG B 624
15
BC6
SOFTWARE
NAG B:624 , FUC B:627 , HOH B:852
BINDING SITE FOR RESIDUE NAG B 625
16
BC7
SOFTWARE
NAG B:624 , NAG B:625
BINDING SITE FOR RESIDUE FUC B 627
17
BC8
SOFTWARE
ARG A:199 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , HOH B:457 , HOH B:471 , HOH B:488 , HOH B:554 , NAG B:678 , HOH B:692 , HOH B:699
BINDING SITE FOR RESIDUE NAG B 677
18
BC9
SOFTWARE
ASP B:19 , GLY B:21 , NAG B:677 , BMA B:679 , MAN B:681
BINDING SITE FOR RESIDUE NAG B 678
19
CC1
SOFTWARE
NAG B:678 , MAN B:680 , MAN B:681
BINDING SITE FOR RESIDUE BMA B 679
20
CC2
SOFTWARE
BMA B:679 , HOH B:737 , HOH B:767 , HOH B:802
BINDING SITE FOR RESIDUE MAN B 680
21
CC3
SOFTWARE
HOH B:608 , NAG B:678 , BMA B:679
BINDING SITE FOR RESIDUE MAN B 681
22
CC4
SOFTWARE
GLU B:383 , ASN B:385 , HOH B:736 , HOH B:764 , HOH B:828
BINDING SITE FOR RESIDUE NAG B 885
23
CC5
SOFTWARE
TRP B:33 , ASP B:78 , ASP B:79 , TYR B:119 , CYS B:127 , MET B:128 , LYS B:154 , ASP B:156 , ARG B:213 , ASP B:217 , HOH B:436 , HOH B:685 , HOH B:725 , HOH B:813 , GLA B:2500
BINDING SITE FOR RESIDUE GLA B 2000
24
CC6
SOFTWARE
CYS B:127 , CYS B:158 , ALA B:191 , TYR B:192 , ASP B:217 , HOH B:612 , GLA B:2000
BINDING SITE FOR RESIDUE GLA B 2500
25
CC7
SOFTWARE
HIS B:110 , GLY B:113 , LEU B:114 , LYS B:115 , ASP B:151 , ARG B:181 , HOH B:552
BINDING SITE FOR RESIDUE CIT B 2100
[
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
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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_d3h55a2 (A:310-404)
1b: SCOP_d3h55b2 (B:310-404)
2a: SCOP_d3h55a1 (A:18-309)
2b: SCOP_d3h55b1 (B:18-309)
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Folds
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(
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Families
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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
d3h55a2
A:310-404
1b
d3h55b2
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
d3h55a1
A:18-309
2b
d3h55b1
B:18-309
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3h55A01 (A:18-307)
1b: CATH_3h55B01 (B:18-307)
2a: CATH_3h55A02 (A:314-404)
2b: CATH_3h55B02 (B:314-404)
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(
)
(
)
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
3h55A01
A:18-307
1b
3h55B01
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
3h55A02
A:314-404
2b
3h55B02
B:314-404
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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