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1XSJ
Asym. Unit
Info
Asym.Unit (779 KB)
Biol.Unit 1 (772 KB)
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(1)
Title
:
STRUCTURE OF A FAMILY 31 ALPHA GLYCOSIDASE
Authors
:
A. L. Lovering, S. S. Lee, Y. W. Kim, S. G. Withers, N. C. Strynadka
Date
:
19 Oct 04 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Beta(8)Alpha(8) Barrel And Beta Sandwich Domains, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. L. Lovering, S. S. Lee, Y. W. Kim, S. G. Withers, N. C. Strynadka
Mechanistic And Structural Analysis Of A Family 31 Alpha-Glycosidase And Its Glycosyl-Enzyme Intermediate
J. Biol. Chem. V. 280 2105 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 12)
Info
All Hetero Components
1a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
1b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
1c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
1d: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSd)
1e: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSe)
1f: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSf)
1g: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSg)
1h: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSh)
1i: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSi)
1j: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSj)
1k: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSk)
1l: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
TRS
12
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:277 , ASP A:306 , LYS A:414 , ASP A:416 , PHE A:417 , ARG A:466 , TRP A:479 , ASP A:482 , PHE A:515 , HIS A:540 , TRS A:2002
BINDING SITE FOR RESIDUE TRS A 2001
02
AC2
SOFTWARE
ASP A:185 , PHE A:417 , ARG A:466 , ASP A:482 , TRS A:2001 , ASP B:49 , TRP D:8
BINDING SITE FOR RESIDUE TRS A 2002
03
AC3
SOFTWARE
ASP B:306 , LYS B:414 , ASP B:416 , PHE B:417 , ARG B:466 , TRP B:479 , ASP B:482 , PHE B:515 , HIS B:540 , TRS B:2004
BINDING SITE FOR RESIDUE TRS B 2003
04
AC4
SOFTWARE
ASP B:185 , TRP B:380 , PHE B:417 , ARG B:466 , ASP B:482 , TRS B:2003 , HOH B:2152 , TRP C:8 , ASP F:49
BINDING SITE FOR RESIDUE TRS B 2004
05
AC5
SOFTWARE
ASP C:306 , LYS C:414 , ASP C:416 , PHE C:417 , ARG C:466 , TRP C:479 , ASP C:482 , PHE C:515 , HIS C:540 , TRS C:2006
BINDING SITE FOR RESIDUE TRS C 2005
06
AC6
SOFTWARE
TRP B:8 , ASP C:185 , PHE C:417 , ARG C:466 , ASP C:482 , TRS C:2005 , HOH C:2232 , ASP D:49
BINDING SITE FOR RESIDUE TRS C 2006
07
AC7
SOFTWARE
TRS A:2008 , ASP D:306 , LYS D:414 , ASP D:416 , PHE D:417 , ARG D:466 , TRP D:479 , ASP D:482 , PHE D:515 , HIS D:540
BINDING SITE FOR RESIDUE TRS D 2007
08
AC8
SOFTWARE
TRP A:8 , ASP D:185 , TRP D:380 , ARG D:466 , ASP D:482 , TRS D:2007 , ASP E:49
BINDING SITE FOR RESIDUE TRS A 2008
09
AC9
SOFTWARE
ASP E:306 , LYS E:414 , ASP E:416 , PHE E:417 , ARG E:466 , TRP E:479 , ASP E:482 , PHE E:515 , HIS E:540 , TRS E:2010
BINDING SITE FOR RESIDUE TRS E 2009
10
BC1
SOFTWARE
ASP C:49 , ASP E:185 , PHE E:417 , ARG E:466 , ASP E:482 , TRS E:2009 , HOH E:2044 , TRP F:8
BINDING SITE FOR RESIDUE TRS E 2010
11
BC2
SOFTWARE
TRS E:2012 , ASP F:306 , LYS F:414 , ASP F:416 , PHE F:417 , ARG F:466 , TRP F:479 , ASP F:482 , PHE F:515 , HIS F:540
BINDING SITE FOR RESIDUE TRS F 2011
12
BC3
SOFTWARE
ASP A:49 , TRP E:8 , ASP F:185 , PHE F:417 , ARG F:466 , ASP F:482 , TRS F:2011 , HOH F:2129
BINDING SITE FOR RESIDUE TRS E 2012
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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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
(4, 24)
Info
All SCOP Domains
1a: SCOP_d1xsja3 (A:586-665)
1b: SCOP_d1xsje3 (E:586-665)
1c: SCOP_d1xsjf3 (F:586-665)
1d: SCOP_d1xsjb3 (B:586-665)
1e: SCOP_d1xsjc3 (C:586-665)
1f: SCOP_d1xsjd3 (D:586-665)
2a: SCOP_d1xsja1 (A:666-773)
2b: SCOP_d1xsje1 (E:666-773)
2c: SCOP_d1xsjf1 (F:666-773)
2d: SCOP_d1xsjb1 (B:666-773)
2e: SCOP_d1xsjc1 (C:666-773)
2f: SCOP_d1xsjd1 (D:666-773)
3a: SCOP_d1xsja2 (A:1-247)
3b: SCOP_d1xsje2 (E:1-247)
3c: SCOP_d1xsjf2 (F:1-247)
3d: SCOP_d1xsjb2 (B:1-247)
3e: SCOP_d1xsjc2 (C:1-247)
3f: SCOP_d1xsjd2 (D:1-247)
4a: SCOP_d1xsja4 (A:248-585)
4b: SCOP_d1xsje4 (E:248-585)
4c: SCOP_d1xsjf4 (F:248-585)
4d: SCOP_d1xsjb4 (B:248-585)
4e: SCOP_d1xsjc4 (C:248-585)
4f: SCOP_d1xsjd4 (D:248-585)
View:
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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
:
Putative glucosidase YicI, domain 3
(5)
Protein domain
:
Putative glucosidase YicI, domain 3
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d1xsja3
A:586-665
1b
d1xsje3
E:586-665
1c
d1xsjf3
F:586-665
1d
d1xsjb3
B:586-665
1e
d1xsjc3
C:586-665
1f
d1xsjd3
D:586-665
Fold
:
Putative glucosidase YicI, C-terminal domain
(5)
Superfamily
:
Putative glucosidase YicI, C-terminal domain
(5)
Family
:
Putative glucosidase YicI, C-terminal domain
(5)
Protein domain
:
Putative glucosidase YicI, C-terminal domain
(5)
Escherichia coli [TaxId: 562]
(5)
2a
d1xsja1
A:666-773
2b
d1xsje1
E:666-773
2c
d1xsjf1
F:666-773
2d
d1xsjb1
B:666-773
2e
d1xsjc1
C:666-773
2f
d1xsjd1
D:666-773
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
YicI N-terminal domain-like
(6)
Protein domain
:
Putative glucosidase YicI, N-terminal domain
(5)
Escherichia coli [TaxId: 562]
(5)
3a
d1xsja2
A:1-247
3b
d1xsje2
E:1-247
3c
d1xsjf2
F:1-247
3d
d1xsjb2
B:1-247
3e
d1xsjc2
C:1-247
3f
d1xsjd2
D:1-247
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
YicI catalytic domain-like
(6)
Protein domain
:
Putative glucosidase YicI, domain 2
(5)
Escherichia coli [TaxId: 562]
(5)
4a
d1xsja4
A:248-585
4b
d1xsje4
E:248-585
4c
d1xsjf4
F:248-585
4d
d1xsjb4
B:248-585
4e
d1xsjc4
C:248-585
4f
d1xsjd4
D:248-585
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Gal_mutarotas_2_1xsjF01 (F:159-219)
1b: PFAM_Gal_mutarotas_2_1xsjF02 (F:159-219)
1c: PFAM_Gal_mutarotas_2_1xsjF03 (F:159-219)
1d: PFAM_Gal_mutarotas_2_1xsjF04 (F:159-219)
1e: PFAM_Gal_mutarotas_2_1xsjF05 (F:159-219)
1f: PFAM_Gal_mutarotas_2_1xsjF06 (F:159-219)
2a: PFAM_Glyco_hydro_31_1xsjF07 (F:239-669)
2b: PFAM_Glyco_hydro_31_1xsjF08 (F:239-669)
2c: PFAM_Glyco_hydro_31_1xsjF09 (F:239-669)
2d: PFAM_Glyco_hydro_31_1xsjF10 (F:239-669)
2e: PFAM_Glyco_hydro_31_1xsjF11 (F:239-669)
2f: PFAM_Glyco_hydro_31_1xsjF12 (F:239-669)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Gal_mutarotase
(81)
Family
:
Gal_mutarotas_2
(11)
Escherichia coli (strain K12)
(3)
1a
Gal_mutarotas_2-1xsjF01
F:159-219
1b
Gal_mutarotas_2-1xsjF02
F:159-219
1c
Gal_mutarotas_2-1xsjF03
F:159-219
1d
Gal_mutarotas_2-1xsjF04
F:159-219
1e
Gal_mutarotas_2-1xsjF05
F:159-219
1f
Gal_mutarotas_2-1xsjF06
F:159-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_31
(25)
Escherichia coli (strain K12)
(3)
2a
Glyco_hydro_31-1xsjF07
F:239-669
2b
Glyco_hydro_31-1xsjF08
F:239-669
2c
Glyco_hydro_31-1xsjF09
F:239-669
2d
Glyco_hydro_31-1xsjF10
F:239-669
2e
Glyco_hydro_31-1xsjF11
F:239-669
2f
Glyco_hydro_31-1xsjF12
F:239-669
[
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (779 KB)
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