PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1XSI
Asym. Unit
Info
Asym.Unit (773 KB)
Biol.Unit 1 (764 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
:
2.20
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, 25)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOa)
2b: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOb)
2c: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOc)
2d: 3[N-MORPHOLINO]PROPANE SULFONIC AC... (MPOd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
3
Ligand/Ion
ACETIC ACID
2
MPO
4
Ligand/Ion
3[N-MORPHOLINO]PROPANE SULFONIC ACID
3
SO4
18
Ligand/Ion
SULFATE ION
[
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
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 , GLN F:757
BINDING SITE FOR RESIDUE SO4 F 3002
03
AC3
SOFTWARE
THR F:246 , LYS F:248 , ARG F:583
BINDING SITE FOR RESIDUE SO4 F 3003
04
AC4
SOFTWARE
THR D:246 , ARG D:583 , HOH D:3068
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 , ARG E:583 , HOH E:3083
BINDING SITE FOR RESIDUE SO4 E 3006
07
AC7
SOFTWARE
THR C:246 , ARG C:583 , HOH C:3142
BINDING SITE FOR RESIDUE SO4 C 3007
08
AC8
SOFTWARE
THR B:246 , LYS B:248 , ALA B:249 , 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 , HIS B:689 , GLN B:757
BINDING SITE FOR RESIDUE SO4 B 3010
11
BC2
SOFTWARE
ASN D:145 , ARG D:147
BINDING SITE FOR RESIDUE SO4 D 3011
12
BC3
SOFTWARE
GLU C:24 , VAL C:25 , ASN C:96 , LYS C:114
BINDING SITE FOR RESIDUE SO4 C 3012
13
BC4
SOFTWARE
ASN B:145 , ARG B:147
BINDING SITE FOR RESIDUE SO4 B 3013
14
BC5
SOFTWARE
ARG A:147 , GLN A:434
BINDING SITE FOR RESIDUE SO4 A 3014
15
BC6
SOFTWARE
ARG B:648 , ARG C:648
BINDING SITE FOR RESIDUE SO4 B 3015
16
BC7
SOFTWARE
VAL B:626 , GLN B:627
BINDING SITE FOR RESIDUE SO4 B 3016
17
BC8
SOFTWARE
THR A:246 , LYS A:248 , ARG A:583
BINDING SITE FOR RESIDUE SO4 A 3017
18
BC9
SOFTWARE
ASN A:145 , ARG A:147
BINDING SITE FOR RESIDUE SO4 A 3018
19
CC1
SOFTWARE
HIS B:640 , ASP B:642 , HIS B:654 , GLY B:655 , SER B:658
BINDING SITE FOR RESIDUE MPO B 1001
20
CC2
SOFTWARE
HIS C:640 , ASP C:642 , GLN C:652 , GLN C:653 , HIS C:654 , GLY C:655
BINDING SITE FOR RESIDUE MPO C 1002
21
CC3
SOFTWARE
HIS D:640 , ASP D:642 , GLN D:652 , GLN D:653 , HIS D:654 , GLY D:655 , SER D:658 , HOH D:3145 , HOH D:3168
BINDING SITE FOR RESIDUE MPO D 1003
22
CC4
SOFTWARE
HIS E:640 , ASP E:642 , GLN E:652 , GLN E:653 , HIS E:654 , GLY E:655 , SER E:658
BINDING SITE FOR RESIDUE MPO E 1004
23
CC5
SOFTWARE
ASP E:306 , LYS E:414 , ASP E:416 , ASP E:482 , PHE E:515 , HIS E:540
BINDING SITE FOR RESIDUE ACY E 2001
24
CC6
SOFTWARE
ASP F:306 , LYS F:414 , ASP F:416 , ASP F:482 , PHE F:515 , HIS F:540
BINDING SITE FOR RESIDUE ACY F 2002
25
CC7
SOFTWARE
PHE A:277 , ASP A:306 , LYS A:414 , ASP A:416 , ASP A:482 , PHE A:515 , HIS A:540
BINDING SITE FOR RESIDUE ACY A 2003
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
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_d1xsia3 (A:586-665)
1b: SCOP_d1xsib3 (B:586-665)
1c: SCOP_d1xsic3 (C:586-665)
1d: SCOP_d1xsid3 (D:586-665)
1e: SCOP_d1xsie3 (E:586-665)
1f: SCOP_d1xsif3 (F:586-665)
2a: SCOP_d1xsia1 (A:666-773)
2b: SCOP_d1xsib1 (B:666-773)
2c: SCOP_d1xsic1 (C:666-773)
2d: SCOP_d1xsid1 (D:666-773)
2e: SCOP_d1xsie1 (E:666-773)
2f: SCOP_d1xsif1 (F:666-773)
3a: SCOP_d1xsia2 (A:1-247)
3b: SCOP_d1xsib2 (B:1-247)
3c: SCOP_d1xsic2 (C:1-247)
3d: SCOP_d1xsid2 (D:1-247)
3e: SCOP_d1xsie2 (E:1-247)
3f: SCOP_d1xsif2 (F:1-247)
4a: SCOP_d1xsia4 (A:248-585)
4b: SCOP_d1xsib4 (B:248-585)
4c: SCOP_d1xsic4 (C:248-585)
4d: SCOP_d1xsid4 (D:248-585)
4e: SCOP_d1xsie4 (E:248-585)
4f: SCOP_d1xsif4 (F:248-585)
View:
Select:
Label:
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
d1xsia3
A:586-665
1b
d1xsib3
B:586-665
1c
d1xsic3
C:586-665
1d
d1xsid3
D:586-665
1e
d1xsie3
E:586-665
1f
d1xsif3
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
d1xsia1
A:666-773
2b
d1xsib1
B:666-773
2c
d1xsic1
C:666-773
2d
d1xsid1
D:666-773
2e
d1xsie1
E:666-773
2f
d1xsif1
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
d1xsia2
A:1-247
3b
d1xsib2
B:1-247
3c
d1xsic2
C:1-247
3d
d1xsid2
D:1-247
3e
d1xsie2
E:1-247
3f
d1xsif2
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
d1xsia4
A:248-585
4b
d1xsib4
B:248-585
4c
d1xsic4
C:248-585
4d
d1xsid4
D:248-585
4e
d1xsie4
E:248-585
4f
d1xsif4
F:248-585
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Gal_mutarotas_2_1xsiF01 (F:159-219)
1b: PFAM_Gal_mutarotas_2_1xsiF02 (F:159-219)
1c: PFAM_Gal_mutarotas_2_1xsiF03 (F:159-219)
1d: PFAM_Gal_mutarotas_2_1xsiF04 (F:159-219)
1e: PFAM_Gal_mutarotas_2_1xsiF05 (F:159-219)
1f: PFAM_Gal_mutarotas_2_1xsiF06 (F:159-219)
2a: PFAM_Glyco_hydro_31_1xsiF07 (F:239-669)
2b: PFAM_Glyco_hydro_31_1xsiF08 (F:239-669)
2c: PFAM_Glyco_hydro_31_1xsiF09 (F:239-669)
2d: PFAM_Glyco_hydro_31_1xsiF10 (F:239-669)
2e: PFAM_Glyco_hydro_31_1xsiF11 (F:239-669)
2f: PFAM_Glyco_hydro_31_1xsiF12 (F:239-669)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Gal_mutarotase
(81)
Family
:
Gal_mutarotas_2
(11)
Escherichia coli (strain K12)
(3)
1a
Gal_mutarotas_2-1xsiF01
F:159-219
1b
Gal_mutarotas_2-1xsiF02
F:159-219
1c
Gal_mutarotas_2-1xsiF03
F:159-219
1d
Gal_mutarotas_2-1xsiF04
F:159-219
1e
Gal_mutarotas_2-1xsiF05
F:159-219
1f
Gal_mutarotas_2-1xsiF06
F:159-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_31
(25)
Escherichia coli (strain K12)
(3)
2a
Glyco_hydro_31-1xsiF07
F:239-669
2b
Glyco_hydro_31-1xsiF08
F:239-669
2c
Glyco_hydro_31-1xsiF09
F:239-669
2d
Glyco_hydro_31-1xsiF10
F:239-669
2e
Glyco_hydro_31-1xsiF11
F:239-669
2f
Glyco_hydro_31-1xsiF12
F:239-669
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (773 KB)
Header - Asym.Unit
Biol.Unit 1 (764 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1XSI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
