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1XSK
Asym. Unit
Info
Asym.Unit (772 KB)
Biol.Unit 1 (764 KB)
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(1)
Title
:
STRUCTURE OF A FAMILY 31 ALPHA GLYCOSIDASE GLYCOSYL-ENZYME INTERMEDIATE
Authors
:
A. L. Lovering, S. S. Lee, Y. W. Kim, S. G. Withers, N. C. Strynadka
Date
:
19 Oct 04 (Deposition) - 10 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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
)
[
close entry info
]
Hetero Components
(3, 21)
Info
All Hetero Components
1a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
1b: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOb)
1c: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOc)
1d: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
3a: 5(R)-5-FLUORO-BETA-D-XYLOPYRANOSYL... (XYFa)
3b: 5(R)-5-FLUORO-BETA-D-XYLOPYRANOSYL... (XYFb)
3c: 5(R)-5-FLUORO-BETA-D-XYLOPYRANOSYL... (XYFc)
3d: 5(R)-5-FLUORO-BETA-D-XYLOPYRANOSYL... (XYFd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MPO
4
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
2
SO4
13
Ligand/Ion
SULFATE ION
3
XYF
4
Ligand/Ion
5(R)-5-FLUORO-BETA-D-XYLOPYRANOSYL-ENZYME INTERMEDIATE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL F:626 , GLN F:627
BINDING SITE FOR RESIDUE SO4 F 3001
02
AC2
SOFTWARE
ARG F:568 , ALA F:687 , HIS F:689
BINDING SITE FOR RESIDUE SO4 F 3002
03
AC3
SOFTWARE
THR F:246 , ARG F:583
BINDING SITE FOR RESIDUE SO4 F 3003
04
AC4
SOFTWARE
THR D:246 , LYS D:248 , ARG D:583 , HOH D:3062
BINDING SITE FOR RESIDUE SO4 D 3004
05
AC5
SOFTWARE
LYS A:403 , TYR F:680 , VAL F:681
BINDING SITE FOR RESIDUE SO4 F 3005
06
AC6
SOFTWARE
THR E:246 , LYS E:248 , ARG E:583 , HOH E:3079
BINDING SITE FOR RESIDUE SO4 E 3006
07
AC7
SOFTWARE
THR C:246 , LYS C:248 , ARG C:583 , HOH C:3139
BINDING SITE FOR RESIDUE SO4 C 3007
08
AC8
SOFTWARE
THR B:246 , ARG B:583
BINDING SITE FOR RESIDUE SO4 B 3008
09
AC9
SOFTWARE
ARG F:333 , ARG F:334
BINDING SITE FOR RESIDUE SO4 F 3009
10
BC1
SOFTWARE
ARG B:568 , ALA B:687 , HIS B:689 , GLN B:757
BINDING SITE FOR RESIDUE SO4 B 3010
11
BC2
SOFTWARE
GLU C:24 , VAL C:25 , ASN C:96 , LYS C:114 , HOH C:3164
BINDING SITE FOR RESIDUE SO4 C 3011
12
BC3
SOFTWARE
ARG A:147 , GLN A:434
BINDING SITE FOR RESIDUE SO4 A 3012
13
BC4
SOFTWARE
THR A:246 , LYS A:248 , ARG A:583 , HOH A:3168
BINDING SITE FOR RESIDUE SO4 A 3013
14
BC5
SOFTWARE
PHE A:277 , ASP A:306 , CYS A:307 , TRP A:345 , TRP A:380 , LYS A:414 , ASP A:416 , PHE A:417 , ARG A:466 , TRP A:479 , ASP A:482 , PHE A:515 , HIS A:540 , HOH A:3174
BINDING SITE FOR RESIDUE XYF A 801
15
BC6
SOFTWARE
PHE B:277 , ASP B:306 , CYS B:307 , TRP B:345 , TRP B:380 , LYS B:414 , ASP B:416 , PHE B:417 , ARG B:466 , TRP B:479 , ASP B:482 , HIS B:540 , HOH B:3122
BINDING SITE FOR RESIDUE XYF B 802
16
BC7
SOFTWARE
PHE C:277 , ASP C:306 , CYS C:307 , TRP C:345 , TRP C:380 , LYS C:414 , ASP C:416 , PHE C:417 , ARG C:466 , TRP C:479 , ASP C:482 , PHE C:515 , HIS C:540 , HOH C:3177
BINDING SITE FOR RESIDUE XYF C 803
17
BC8
SOFTWARE
PHE E:277 , ASP E:306 , CYS E:307 , TRP E:345 , TRP E:380 , LYS E:414 , ASP E:416 , PHE E:417 , ARG E:466 , TRP E:479 , ASP E:482 , PHE E:515 , HIS E:540 , HOH E:3076
BINDING SITE FOR RESIDUE XYF E 804
18
BC9
SOFTWARE
HIS B:640 , ASP B:642 , GLN B:653 , HIS B:654 , GLY B:655 , SER B:658
BINDING SITE FOR RESIDUE MPO B 2001
19
CC1
SOFTWARE
HIS C:640 , GLN C:653 , HIS C:654 , GLY C:655 , SER C:658
BINDING SITE FOR RESIDUE MPO C 2002
20
CC2
SOFTWARE
HIS D:640 , ASP D:642 , GLN D:653 , HIS D:654 , GLY D:655 , HOH D:3134
BINDING SITE FOR RESIDUE MPO D 2003
21
CC3
SOFTWARE
ARG D:296 , HIS E:640 , ASP E:642 , GLN E:652 , GLN E:653 , GLY E:655
BINDING SITE FOR RESIDUE MPO E 2004
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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_d1xska3 (A:586-665)
1b: SCOP_d1xskb3 (B:586-665)
1c: SCOP_d1xskc3 (C:586-665)
1d: SCOP_d1xskd3 (D:586-665)
1e: SCOP_d1xske3 (E:586-665)
1f: SCOP_d1xskf3 (F:586-665)
2a: SCOP_d1xska1 (A:666-773)
2b: SCOP_d1xskb1 (B:666-773)
2c: SCOP_d1xskc1 (C:666-773)
2d: SCOP_d1xskd1 (D:666-773)
2e: SCOP_d1xske1 (E:666-773)
2f: SCOP_d1xskf1 (F:666-773)
3a: SCOP_d1xska2 (A:1-247)
3b: SCOP_d1xskb2 (B:1-247)
3c: SCOP_d1xskc2 (C:1-247)
3d: SCOP_d1xskd2 (D:1-247)
3e: SCOP_d1xske2 (E:1-247)
3f: SCOP_d1xskf2 (F:1-247)
4a: SCOP_d1xska4 (A:248-585)
4b: SCOP_d1xskb4 (B:248-585)
4c: SCOP_d1xskc4 (C:248-585)
4d: SCOP_d1xskd4 (D:248-585)
4e: SCOP_d1xske4 (E:248-585)
4f: SCOP_d1xskf4 (F: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
d1xska3
A:586-665
1b
d1xskb3
B:586-665
1c
d1xskc3
C:586-665
1d
d1xskd3
D:586-665
1e
d1xske3
E:586-665
1f
d1xskf3
F: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
d1xska1
A:666-773
2b
d1xskb1
B:666-773
2c
d1xskc1
C:666-773
2d
d1xskd1
D:666-773
2e
d1xske1
E:666-773
2f
d1xskf1
F: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
d1xska2
A:1-247
3b
d1xskb2
B:1-247
3c
d1xskc2
C:1-247
3d
d1xskd2
D:1-247
3e
d1xske2
E:1-247
3f
d1xskf2
F: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
d1xska4
A:248-585
4b
d1xskb4
B:248-585
4c
d1xskc4
C:248-585
4d
d1xskd4
D:248-585
4e
d1xske4
E:248-585
4f
d1xskf4
F:248-585
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Gal_mutarotas_2_1xskF01 (F:159-219)
1b: PFAM_Gal_mutarotas_2_1xskF02 (F:159-219)
1c: PFAM_Gal_mutarotas_2_1xskF03 (F:159-219)
1d: PFAM_Gal_mutarotas_2_1xskF04 (F:159-219)
1e: PFAM_Gal_mutarotas_2_1xskF05 (F:159-219)
1f: PFAM_Gal_mutarotas_2_1xskF06 (F:159-219)
2a: PFAM_Glyco_hydro_31_1xskF07 (F:239-669)
2b: PFAM_Glyco_hydro_31_1xskF08 (F:239-669)
2c: PFAM_Glyco_hydro_31_1xskF09 (F:239-669)
2d: PFAM_Glyco_hydro_31_1xskF10 (F:239-669)
2e: PFAM_Glyco_hydro_31_1xskF11 (F:239-669)
2f: PFAM_Glyco_hydro_31_1xskF12 (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_2-1xskF01
F:159-219
1b
Gal_mutarotas_2-1xskF02
F:159-219
1c
Gal_mutarotas_2-1xskF03
F:159-219
1d
Gal_mutarotas_2-1xskF04
F:159-219
1e
Gal_mutarotas_2-1xskF05
F:159-219
1f
Gal_mutarotas_2-1xskF06
F:159-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_31
(25)
Escherichia coli (strain K12)
(3)
2a
Glyco_hydro_31-1xskF07
F:239-669
2b
Glyco_hydro_31-1xskF08
F:239-669
2c
Glyco_hydro_31-1xskF09
F:239-669
2d
Glyco_hydro_31-1xskF10
F:239-669
2e
Glyco_hydro_31-1xskF11
F:239-669
2f
Glyco_hydro_31-1xskF12
F:239-669
[
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]
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Asym.Unit (772 KB)
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