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1KTC
Biol. Unit 1
Info
Asym.Unit (79 KB)
Biol.Unit 1 (143 KB)
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(1)
Title
:
THE STRUCTURE OF ALPHA-N-ACETYLGALACTOSAMINIDASE
Authors
:
S. C. Garman, L. Hannick, A. Zhu, D. N. Garboczi
Date
:
15 Jan 02 (Deposition) - 15 Mar 02 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Glycoprotein, (Beta/Alpha)8 Barrel, Protein-Ligand Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. C. Garman, L. Hannick, A. Zhu, D. N. Garboczi
The 1. 9 A Structure Of Alpha-N-Acetylgalactosaminidase: Molecular Basis Of Glycosidase Deficiency Diseases.
Structure V. 10 425 2002
[
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Hetero Components
(5, 44)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4a: N-ACETYL-D-GALACTOSAMINE (NGAa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
4
Ligand/Ion
ACETIC ACID
2
GOL
20
Ligand/Ion
GLYCEROL
3
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NGA
2
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
5
SO4
10
Ligand/Ion
SULFATE ION
[
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]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:3 , ASN A:161 , GLY A:164 , ARG A:165 , NAG A:662 , HOH A:3197 , HOH A:3239
BINDING SITE FOR RESIDUE NAG A 661
02
AC2
SOFTWARE
GLY A:4 , NAG A:661
BINDING SITE FOR RESIDUE NAG A 662
03
AC3
SOFTWARE
ASN A:185 , LEU A:188 , GLU A:191
BINDING SITE FOR RESIDUE NAG A 685
04
AC4
SOFTWARE
THR A:336 , ASN A:369
BINDING SITE FOR RESIDUE NAG A 869
05
AC5
SOFTWARE
TRP A:16 , ASP A:61 , ASP A:62 , TYR A:103 , CYS A:111 , LYS A:138 , ASP A:140 , SER A:172 , ARG A:197 , ASP A:201 , HOH A:3108 , HOH A:3227 , HOH A:3284
BINDING SITE FOR RESIDUE NGA A 870
06
AC6
SOFTWARE
GLU A:27 , ASP A:28 , PRO A:29 , ARG A:30 , GLN A:31 , HOH A:3183 , HOH A:3215 , HOH A:3218
BINDING SITE FOR RESIDUE SO4 A 2101
07
AC7
SOFTWARE
SER A:145 , GLY A:146 , GLN A:177 , LYS A:341 , HOH A:3243 , HOH A:3303
BINDING SITE FOR RESIDUE SO4 A 2102
08
AC8
SOFTWARE
ARG A:251 , SER A:357 , HOH A:3317
BINDING SITE FOR RESIDUE SO4 A 2103
09
AC9
SOFTWARE
HIS A:307 , ARG A:327 , HOH A:3195 , HOH A:3306
BINDING SITE FOR RESIDUE SO4 A 2104
10
BC1
SOFTWARE
ARG A:51 , ARG A:96
BINDING SITE FOR RESIDUE SO4 A 2105
11
BC2
SOFTWARE
ASP A:354 , LYS A:359 , THR A:371 , TRP A:382 , HOH A:3225 , HOH A:3255 , HOH A:3391
BINDING SITE FOR RESIDUE GOL A 1103
12
BC3
SOFTWARE
GLN A:220 , ASP A:221 , ARG A:299 , GOL A:1110 , HOH A:3242
BINDING SITE FOR RESIDUE GOL A 1104
13
BC4
SOFTWARE
PRO A:77 , ARG A:84 , GLY A:85 , ILE A:86 , LYS A:87 , ALA A:88 , TRP A:132
BINDING SITE FOR RESIDUE GOL A 1105
14
BC5
SOFTWARE
GLN A:317 , TYR A:383 , CYS A:385
BINDING SITE FOR RESIDUE GOL A 1106
15
BC6
SOFTWARE
SER A:316 , GLN A:317 , HOH A:3293
BINDING SITE FOR RESIDUE GOL A 1107
16
BC7
SOFTWARE
ARG A:108 , TYR A:143 , ILE A:301 , LYS A:341 , LEU A:342
BINDING SITE FOR RESIDUE GOL A 1108
17
BC8
SOFTWARE
TRP A:215 , ASN A:219 , HOH A:3130 , HOH A:3157 , HOH A:3176 , HOH A:3312
BINDING SITE FOR RESIDUE GOL A 1109
18
BC9
SOFTWARE
PHE A:217 , GLN A:220 , ARG A:300 , LYS A:303 , GOL A:1104
BINDING SITE FOR RESIDUE GOL A 1110
19
CC1
SOFTWARE
CYS A:111 , GLY A:113 , TYR A:143 , LEU A:312 , PRO A:314 , ALA A:318 , ALA A:319 , SER A:320 , HOH A:3164 , HOH A:3258 , HOH A:3300
BINDING SITE FOR RESIDUE GOL A 1101
20
CC2
SOFTWARE
ILE A:361 , PHE A:370 , THR A:371 , HOH A:3192 , HOH A:3365 , HOH A:3391
BINDING SITE FOR RESIDUE GOL A 1102
21
CC3
SOFTWARE
GLN A:282 , ASN A:283 , ARG A:284 , HOH A:3185 , HOH A:3342
BINDING SITE FOR RESIDUE ACY A 3101
22
CC4
SOFTWARE
HIS A:94 , ARG A:165
BINDING SITE FOR RESIDUE ACY A 3102
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ALPHA_GALACTOSIDASE (A:54-70)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALPHA_GALACTOSIDASE
PS00512
Alpha-galactosidase signature.
NAGAB_CHICK
54-70
2
A:54-70
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ktca1 (A:294-388)
2a: SCOP_d1ktca2 (A:1-293)
View:
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Classes
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)
(
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Folds
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(
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Superfamilies
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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
:
alpha-Amylases, C-terminal beta-sheet domain
(272)
Protein domain
:
Melibiase
(21)
Chicken (Gallus gallus) [TaxId: 9031]
(2)
1a
d1ktca1
A:294-388
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
:
Melibiase
(21)
Chicken (Gallus gallus) [TaxId: 9031]
(2)
2a
d1ktca2
A:1-293
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1ktcA01 (A:1-291)
2a: CATH_1ktcA02 (A:298-388)
View:
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(
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Architectures
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(
)
Topologies
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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)
Chicken (Gallus gallus)
(18)
1a
1ktcA01
A:1-291
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Chicken (Gallus gallus)
(2)
2a
1ktcA02
A:298-388
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Melibiase_1ktcA01 (A:2-120)
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Clans
(
)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Melibiase
(11)
Gallus gallus (Chicken)
(2)
1a
Melibiase-1ktcA01
A:2-120
[
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]
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Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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