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1X9D
Asym. Unit
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Asym.Unit (88 KB)
Biol.Unit 1 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA-1,2-MANNOSIDASE IN COMPLEX WITH THIO-DISACCHARIDE SUBSTRATE ANALOGUE
Authors
:
K. Karaveg, W. Tempel, Z. J. Liu, A. Siriwardena, K. W. Moremen, B. C. Wang
Date
:
20 Aug 04 (Deposition) - 22 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.41
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Mannosidase, Substrate Analogue, Glycosyl Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Karaveg, A. Siriwardena, W. Tempel, Z. J. Liu, J. Glushka, B. C. Wang, K. W. Moremen
Mechanism Of Class 1 (Glycosylhydrolase Family 47) {Alpha}-Mannosidases Involved In N-Glycan Processing And Endoplasmic Reticulum Quality Control.
J. Biol. Chem. V. 280 16197 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 4)
Info
All Hetero Components
1a: 1,4-BUTANEDIOL (BU1a)
2a: CALCIUM ION (CAa)
3a: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDa)
4a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BU1
1
Ligand/Ion
1,4-BUTANEDIOL
2
CA
1
Ligand/Ion
CALCIUM ION
3
SMD
1
Ligand/Ion
METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D-MANNOPYRANOSIDE
4
SO4
1
Ligand/Ion
SULFATE ION
[
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]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:688 , SMD A:1003 , HOH A:1005 , HOH A:1008 , HOH A:1009 , HOH A:1010
BINDING SITE FOR RESIDUE CA A 1001
2
AC2
SOFTWARE
LYS A:262 , LYS A:266 , THR A:451 , HIS A:452 , LEU A:453
BINDING SITE FOR RESIDUE SO4 A 1002
3
AC3
SOFTWARE
ARG A:334 , ALA A:396 , GLU A:397 , ARG A:461 , ASP A:463 , LEU A:525 , ARG A:597 , PRO A:598 , GLU A:599 , GLU A:663 , THR A:688 , GLU A:689 , CA A:1001 , HOH A:1009 , HOH A:1010 , HOH A:1012 , HOH A:1021 , HOH A:1302
BINDING SITE FOR RESIDUE SMD A 1003
4
AC4
SOFTWARE
GLY A:302 , HIS A:429 , GLY A:430 , SER A:432 , HOH A:1057 , HOH A:1067
BINDING SITE FOR RESIDUE BU1 A 1004
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066592 (R334C, chain A, )
2: VAR_066593 (E397K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066592
R
334
C
MA1B1_HUMAN
Disease (MRT15)
---
A
R
334
C
2
UniProt
VAR_066593
E
397
K
MA1B1_HUMAN
Disease (MRT15)
---
A
E
397
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(8, 8)
Info
All Exons
Exon 1.8 (A:245-306)
Exon 1.9 (A:306-355)
Exon 1.10a (A:356-418)
Exon 1.11b (A:419-482)
Exon 1.12 (A:482-522)
Exon 1.13a (A:523-588)
Exon 1.14a (A:589-632)
Exon 1.14d (A:633-697 (gaps))
View:
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All Exon Boundaries
1: Boundary 1.7/1.8
2: Boundary 1.8/1.9
3: Boundary 1.9/1.10a
4: Boundary 1.10a/1.11b
5: Boundary 1.11b/1.12
6: Boundary 1.12/1.13a
7: Boundary 1.13a/1.14a
8: Boundary 1.14a/1.14d
9: Boundary 1.14d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000371589
1a
ENSE00001455607
chr9:
139981400-139981670
271
MA1B1_HUMAN
1-73
73
0
-
-
1.2
ENST00000371589
2
ENSE00001792863
chr9:
139982527-139982635
109
MA1B1_HUMAN
74-110
37
0
-
-
1.4
ENST00000371589
4
ENSE00001280716
chr9:
139983321-139983457
137
MA1B1_HUMAN
110-155
46
0
-
-
1.6
ENST00000371589
6
ENSE00001280706
chr9:
139990689-139990843
155
MA1B1_HUMAN
156-207
52
0
-
-
1.7
ENST00000371589
7
ENSE00001280699
chr9:
139992280-139992389
110
MA1B1_HUMAN
207-244
38
0
-
-
1.8
ENST00000371589
8
ENSE00001280694
chr9:
139994148-139994333
186
MA1B1_HUMAN
244-306
63
1
A:245-306
62
1.9
ENST00000371589
9
ENSE00001280687
chr9:
139995457-139995605
149
MA1B1_HUMAN
306-355
50
1
A:306-355
50
1.10a
ENST00000371589
10a
ENSE00001280681
chr9:
139995936-139996124
189
MA1B1_HUMAN
356-418
63
1
A:356-418
63
1.11b
ENST00000371589
11b
ENSE00001280672
chr9:
140000577-140000767
191
MA1B1_HUMAN
419-482
64
1
A:419-482
64
1.12
ENST00000371589
12
ENSE00001280664
chr9:
140001141-140001261
121
MA1B1_HUMAN
482-522
41
1
A:482-522
41
1.13a
ENST00000371589
13a
ENSE00001280655
chr9:
140001702-140001899
198
MA1B1_HUMAN
523-588
66
1
A:523-588
66
1.14a
ENST00000371589
14a
ENSE00001280645
chr9:
140001983-140002114
132
MA1B1_HUMAN
589-632
44
1
A:589-632
44
1.14d
ENST00000371589
14d
ENSE00001810926
chr9:
140002840-140003635
796
MA1B1_HUMAN
633-699
67
1
A:633-697 (gaps)
65
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1x9da_ (A:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha/alpha toroid
(324)
Superfamily
:
Seven-hairpin glycosidases
(13)
Family
:
Class I alpha-1;2-mannosidase, catalytic domain
(13)
Protein domain
:
Class I alpha-1;2-mannosidase, catalytic domain
(13)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1x9da_
A:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1x9dA00 (A:245-697)
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha/alpha barrel
(251)
Topology
:
Glycosyltransferase
(233)
Homologous Superfamily
:
[code=1.50.10.50, no name defined]
(13)
Human (Homo sapiens)
(4)
1a
1x9dA00
A:245-697
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_47_1x9dA01 (A:256-695)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
Glyco_hydro_47
(6)
Homo sapiens (Human)
(1)
1a
Glyco_hydro_47-1x9dA01
A:256-695
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