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...
Getting 'PROSITE' information from database.
1O7A
Biol. Unit 3
Info
Asym.Unit (539 KB)
Biol.Unit 1 (182 KB)
Biol.Unit 2 (180 KB)
Biol.Unit 3 (97 KB)
Biol.Unit 4 (182 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN BETA-HEXOSAMINIDASE B
Authors
:
T. Maier, N. Strater, C. Schuette, R. Klingenstein, K. Sandhoff, W. Saenger
Date
:
29 Oct 02 (Deposition) - 23 Oct 03 (Release) - 25 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E (1x)
Biol. Unit 4: F (2x)
Keywords
:
Hydrolase, Glycosyl Hydrolase, Hexosaminidase, Lysosomal, Sphingolipid Degradation, Sandhoff Disease, Ba8-Barrel, Glycosidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Maier, N. Strater, C. Schuette, R. Klingenstein, K. Sandhoff, W. Saenger
The X-Ray Crystal Structure Of Human Beta-Hexosaminidase B Provides New Insights Into Sandhoff Disease
J. Mol. Biol. V. 328 669 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
2a: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLa)
2b: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLb)
2c: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLc)
2d: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLd)
2e: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLe)
2f: 2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-... (GDLf)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
2
GDL
1
Ligand/Ion
2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
3
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC6 (SOFTWARE)
2: BC5 (SOFTWARE)
3: BC6 (SOFTWARE)
4: BC7 (SOFTWARE)
5: BC8 (SOFTWARE)
6: CC2 (SOFTWARE)
7: DC2 (SOFTWARE)
8: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
TRP B:424 , LYS B:425 , ASP B:426 , TYR B:450 , HOH B:2399 , ARG E:372
BINDING SITE FOR RESIDUE EDO B 800
2
BC5
SOFTWARE
ARG E:211 , HIS E:294 , ASP E:354 , GLU E:355 , TRP E:405 , TRP E:424 , TYR E:450 , ASP E:452 , TRP E:489 , GLU E:491 , HOH E:2442 , HOH E:2443 , HOH E:2444 , HOH E:2445
BINDING SITE FOR RESIDUE GDL E 600
3
BC6
SOFTWARE
TRP E:424 , LYS E:425 , ASP E:426 , ALA E:447 , TYR E:450 , LEU E:453
BINDING SITE FOR RESIDUE EDO E 800
4
BC7
SOFTWARE
PHE E:77 , TYR E:78 , ILE E:79 , PHE E:98 , HIS E:102
BINDING SITE FOR RESIDUE EDO E 801
5
BC8
SOFTWARE
GLY E:457 , GLN E:458 , ASP E:459 , TRP E:460 , ARG E:505 , PRO E:545 , LEU E:546
BINDING SITE FOR RESIDUE EDO E 802
6
CC2
SOFTWARE
LEU E:262 , TYR F:78 , ILE F:79 , HIS F:102
BINDING SITE FOR RESIDUE EDO F 801
7
DC2
SOFTWARE
PRO E:83 , ASN E:84
BINDING SITE FOR MONO-SACCHARIDE NAG E 702 BOUND TO ASN E 84
8
DC3
SOFTWARE
MET E:65 , THR E:66 , PRO E:67 , LEU E:69 , ASN E:190 , HOH E:2446
BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E 190 RESIDUES 700 TO 701
[
close Site info
]
SAPs(SNPs)/Variants
(10, 10)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_003247 (S62L, chain E, )
02: VAR_003249 (I207V, chain E, )
03: VAR_011704 (S255R, chain E, )
04: VAR_003250 (C309Y, chain E, )
05: VAR_003251 (P417L, chain E, )
06: VAR_003252 (Y456S, chain E, )
07: VAR_011705 (P504S, chain E, )
08: VAR_003253 (R505Q, chain E, )
09: VAR_003254 (C534Y, chain E, )
10: VAR_011706 (A543T, chain E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_003247
S
62
L
HEXB_HUMAN
Disease (GM2G2)
820878
E
S
62
L
02
UniProt
VAR_003249
I
207
V
HEXB_HUMAN
Polymorphism
10805890
E
I
207
V
03
UniProt
VAR_011704
S
255
R
HEXB_HUMAN
Disease (GM2G2)
---
E
S
255
R
04
UniProt
VAR_003250
C
309
Y
HEXB_HUMAN
Disease (GM2G2)
---
E
C
309
Y
05
UniProt
VAR_003251
P
417
L
HEXB_HUMAN
Disease (GM2G2)
28942073
E
P
417
L
06
UniProt
VAR_003252
Y
456
S
HEXB_HUMAN
Disease (GM2G2)
---
E
Y
456
S
07
UniProt
VAR_011705
P
504
S
HEXB_HUMAN
Disease (GM2G2)
---
E
P
504
S
08
UniProt
VAR_003253
R
505
Q
HEXB_HUMAN
Disease (GM2G2)
---
E
R
505
Q
09
UniProt
VAR_003254
C
534
Y
HEXB_HUMAN
Disease (GM2G2)
---
E
C
534
Y
10
UniProt
VAR_011706
A
543
T
HEXB_HUMAN
Disease (GM2G2)
---
E
A
543
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1o7aa2 (A:54-199)
1b: SCOP_d1o7ab2 (B:54-199)
1c: SCOP_d1o7ac2 (C:54-199)
1d: SCOP_d1o7ad2 (D:54-199)
1e: SCOP_d1o7ae2 (E:54-199)
1f: SCOP_d1o7af2 (F:54-199)
2a: SCOP_d1o7aa1 (A:200-554)
2b: SCOP_d1o7ab1 (B:200-554)
2c: SCOP_d1o7ac1 (C:200-554)
2d: SCOP_d1o7ad1 (D:200-553)
2e: SCOP_d1o7ae1 (E:200-554)
2f: SCOP_d1o7af1 (F:200-554)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
beta-N-acetylhexosaminidase-like domain
(54)
Family
:
beta-N-acetylhexosaminidase domain
(18)
Protein domain
:
beta-hexosaminidase B, N-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1o7aa2
A:54-199
1b
d1o7ab2
B:54-199
1c
d1o7ac2
C:54-199
1d
d1o7ad2
D:54-199
1e
d1o7ae2
E:54-199
1f
d1o7af2
F:54-199
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-N-acetylhexosaminidase catalytic domain
(22)
Protein domain
:
beta-hexosaminidase B
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
2a
d1o7aa1
A:200-554
2b
d1o7ab1
B:200-554
2c
d1o7ac1
C:200-554
2d
d1o7ad1
D:200-553
2e
d1o7ae1
E:200-554
2f
d1o7af1
F:200-554
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1o7aA01 (A:55-197)
1b: CATH_1o7aB01 (B:55-197)
1c: CATH_1o7aC01 (C:55-197)
1d: CATH_1o7aD01 (D:55-197)
1e: CATH_1o7aE01 (E:55-197)
1f: CATH_1o7aF01 (F:55-197)
2a: CATH_1o7aA02 (A:198-552)
2b: CATH_1o7aB02 (B:198-552)
2c: CATH_1o7aC02 (C:198-552)
2d: CATH_1o7aD02 (D:198-552)
2e: CATH_1o7aE02 (E:198-552)
2f: CATH_1o7aF02 (F:198-552)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Chitobiase; domain 2
(28)
Homologous Superfamily
:
Chitobiase, domain 2
(28)
Human (Homo sapiens)
(6)
1a
1o7aA01
A:55-197
1b
1o7aB01
B:55-197
1c
1o7aC01
C:55-197
1d
1o7aD01
D:55-197
1e
1o7aE01
E:55-197
1f
1o7aF01
F:55-197
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Human (Homo sapiens)
(94)
2a
1o7aA02
A:198-552
2b
1o7aB02
B:198-552
2c
1o7aC02
C:198-552
2d
1o7aD02
D:198-552
2e
1o7aE02
E:198-552
2f
1o7aF02
F:198-552
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_20_1o7aF01 (F:200-517)
1b: PFAM_Glyco_hydro_20_1o7aF02 (F:200-517)
1c: PFAM_Glyco_hydro_20_1o7aF03 (F:200-517)
1d: PFAM_Glyco_hydro_20_1o7aF04 (F:200-517)
1e: PFAM_Glyco_hydro_20_1o7aF05 (F:200-517)
1f: PFAM_Glyco_hydro_20_1o7aF06 (F:200-517)
2a: PFAM_Glyco_hydro_20b_1o7aF07 (F:68-198)
2b: PFAM_Glyco_hydro_20b_1o7aF08 (F:68-198)
2c: PFAM_Glyco_hydro_20b_1o7aF09 (F:68-198)
2d: PFAM_Glyco_hydro_20b_1o7aF10 (F:68-198)
2e: PFAM_Glyco_hydro_20b_1o7aF11 (F:68-198)
2f: PFAM_Glyco_hydro_20b_1o7aF12 (F:68-198)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_20
(9)
Homo sapiens (Human)
(4)
1a
Glyco_hydro_20-1o7aF01
F:200-517
1b
Glyco_hydro_20-1o7aF02
F:200-517
1c
Glyco_hydro_20-1o7aF03
F:200-517
1d
Glyco_hydro_20-1o7aF04
F:200-517
1e
Glyco_hydro_20-1o7aF05
F:200-517
1f
Glyco_hydro_20-1o7aF06
F:200-517
Clan
:
no clan defined [family: Glyco_hydro_20b]
(22)
Family
:
Glyco_hydro_20b
(22)
Homo sapiens (Human)
(4)
2a
Glyco_hydro_20b-1o7aF07
F:68-198
2b
Glyco_hydro_20b-1o7aF08
F:68-198
2c
Glyco_hydro_20b-1o7aF09
F:68-198
2d
Glyco_hydro_20b-1o7aF10
F:68-198
2e
Glyco_hydro_20b-1o7aF11
F:68-198
2f
Glyco_hydro_20b-1o7aF12
F:68-198
[
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 E
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 (539 KB)
Header - Asym.Unit
Biol.Unit 1 (182 KB)
Header - Biol.Unit 1
Biol.Unit 2 (180 KB)
Header - Biol.Unit 2
Biol.Unit 3 (97 KB)
Header - Biol.Unit 3
Biol.Unit 4 (182 KB)
Header - Biol.Unit 4
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
1O7A
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help