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.
1K0U
Biol. Unit 1
Info
Asym.Unit (531 KB)
Biol.Unit 1 (268 KB)
Biol.Unit 2 (264 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
INHIBITION OF S-ADENOSYLHOMOCYSTEINE HYDROLASE BY "ACYCLIC SUGAR" ADENOSINE ANALOGUE D-ERITADENINE
Authors
:
F. Takusagawa, Y. Huang, J. Komoto, Y. Takata, T. Gomi, H. Ogawa, M. Fujioka, D. Powell
Date
:
20 Sep 01 (Deposition) - 17 Oct 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
S-Adenosylhomocysteine, Hydrolase, D-Eritadenine, Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Huang, J. Komoto, Y. Takata, D. R. Powell, T. Gomi, H. Ogawa, M. Fujioka, F. Takusagawa
Inhibition Of S-Adenosylhomocysteine Hydrolase By Acyclic Sugar Adenosine Analogue D-Eritadenine. Crystal Structure Of S-Adenosylhomocysteine Hydrolase Complexed With D-Eritadenine.
J. Biol. Chem. V. 277 7477 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: D-ERITADENINE (DEAa)
1b: D-ERITADENINE (DEAb)
1c: D-ERITADENINE (DEAc)
1d: D-ERITADENINE (DEAd)
1e: D-ERITADENINE (DEAe)
1f: D-ERITADENINE (DEAf)
1g: D-ERITADENINE (DEAg)
1h: D-ERITADENINE (DEAh)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DEA
4
Ligand/Ion
D-ERITADENINE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:156 , THR A:157 , THR A:158 , ASN A:190 , GLY A:219 , GLY A:221 , ASP A:222 , VAL A:223 , THR A:241 , GLU A:242 , ILE A:243 , ASP A:244 , ASN A:247 , THR A:274 , THR A:275 , ILE A:280 , ILE A:298 , GLY A:299 , HIS A:300 , LEU A:343 , ASN A:345 , HIS A:352 , DEA A:1433 , HOH A:9224 , GLN B:412 , LYS B:425 , TYR B:429
BINDING SITE FOR RESIDUE NAD A 1432
2
AC2
SOFTWARE
HIS A:54 , THR A:56 , GLU A:58 , THR A:59 , ASP A:130 , GLU A:155 , THR A:156 , LYS A:185 , ASP A:189 , LEU A:346 , GLY A:351 , HIS A:352 , PHE A:361 , NAD A:1432
BINDING SITE FOR RESIDUE DEA A 1433
3
AC3
SOFTWARE
GLN A:412 , LYS A:425 , TYR A:429 , THR B:156 , THR B:157 , THR B:158 , ASN B:190 , GLY B:219 , GLY B:221 , ASP B:222 , VAL B:223 , THR B:241 , GLU B:242 , ILE B:243 , ASP B:244 , ASN B:247 , THR B:274 , THR B:275 , ILE B:280 , ILE B:298 , GLY B:299 , HIS B:300 , LEU B:343 , ASN B:345 , HIS B:352 , DEA B:2433 , HOH B:9363
BINDING SITE FOR RESIDUE NAD B 2432
4
AC4
SOFTWARE
HIS B:54 , THR B:56 , GLU B:58 , THR B:59 , ASP B:130 , GLU B:155 , THR B:156 , LYS B:185 , ASP B:189 , LEU B:346 , GLY B:351 , HIS B:352 , PHE B:361 , NAD B:2432
BINDING SITE FOR RESIDUE DEA B 2433
5
AC5
SOFTWARE
THR C:156 , THR C:157 , THR C:158 , ASN C:190 , GLY C:219 , GLY C:221 , ASP C:222 , VAL C:223 , THR C:241 , GLU C:242 , ILE C:243 , ASP C:244 , ASN C:247 , THR C:274 , THR C:275 , ILE C:280 , ILE C:298 , GLY C:299 , HIS C:300 , LEU C:343 , ASN C:345 , HIS C:352 , DEA C:3433 , GLN D:412 , LYS D:425 , TYR D:429
BINDING SITE FOR RESIDUE NAD C 3432
6
AC6
SOFTWARE
HIS C:54 , THR C:56 , GLU C:58 , THR C:59 , ASP C:130 , GLU C:155 , THR C:156 , LYS C:185 , ASP C:189 , LEU C:346 , GLY C:351 , HIS C:352 , MET C:357 , PHE C:361 , NAD C:3432
BINDING SITE FOR RESIDUE DEA C 3433
7
AC7
SOFTWARE
GLN C:412 , LYS C:425 , TYR C:429 , THR D:156 , THR D:157 , THR D:158 , ASN D:190 , GLY D:219 , GLY D:221 , ASP D:222 , VAL D:223 , THR D:241 , GLU D:242 , ILE D:243 , ASP D:244 , ASN D:247 , THR D:274 , THR D:275 , ILE D:280 , ILE D:298 , GLY D:299 , HIS D:300 , LEU D:343 , ASN D:345 , HIS D:352 , DEA D:4433
BINDING SITE FOR RESIDUE NAD D 4432
8
AC8
SOFTWARE
HIS D:54 , THR D:56 , GLU D:58 , THR D:59 , ASP D:130 , GLU D:155 , THR D:156 , LYS D:185 , ASP D:189 , LEU D:346 , GLY D:351 , HIS D:352 , MET D:357 , PHE D:361 , NAD D:4432
BINDING SITE FOR RESIDUE DEA D 4433
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ADOHCYASE_1 (A:77-91,B:77-91,C:77-91,D:77-91)
2: ADOHCYASE_2 (A:212-228,B:212-228,C:212-228,D:21...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOHCYASE_1
PS00738
S-adenosyl-L-homocysteine hydrolase signature 1.
SAHH_RAT
78-92
4
A:77-91
B:77-91
C:77-91
D:77-91
-
-
-
-
2
ADOHCYASE_2
PS00739
S-adenosyl-L-homocysteine hydrolase signature 2.
SAHH_RAT
213-229
4
A:212-228
B:212-228
C:212-228
D:212-228
-
-
-
-
[
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, 16)
Info
All SCOP Domains
1a: SCOP_d1k0ua2 (A:2-189,A:353-431)
1b: SCOP_d1k0ug2 (G:2-189,G:353-431)
1c: SCOP_d1k0uh2 (H:2-189,H:353-431)
1d: SCOP_d1k0ub2 (B:2-189,B:353-431)
1e: SCOP_d1k0uc2 (C:2-189,C:353-431)
1f: SCOP_d1k0ud2 (D:2-189,D:353-431)
1g: SCOP_d1k0ue2 (E:2-189,E:353-431)
1h: SCOP_d1k0uf2 (F:2-189,F:353-431)
2a: SCOP_d1k0ua1 (A:190-352)
2b: SCOP_d1k0ug1 (G:190-352)
2c: SCOP_d1k0uh1 (H:190-352)
2d: SCOP_d1k0ub1 (B:190-352)
2e: SCOP_d1k0uc1 (C:190-352)
2f: SCOP_d1k0ud1 (D:190-352)
2g: SCOP_d1k0ue1 (E:190-352)
2h: SCOP_d1k0uf1 (F:190-352)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
S-adenosylhomocystein hydrolase
(10)
Protein domain
:
S-adenosylhomocystein hydrolase
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(7)
1a
d1k0ua2
A:2-189,A:353-431
1b
d1k0ug2
G:2-189,G:353-431
1c
d1k0uh2
H:2-189,H:353-431
1d
d1k0ub2
B:2-189,B:353-431
1e
d1k0uc2
C:2-189,C:353-431
1f
d1k0ud2
D:2-189,D:353-431
1g
d1k0ue2
E:2-189,E:353-431
1h
d1k0uf2
F:2-189,F:353-431
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
S-adenosylhomocystein hydrolase
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(7)
2a
d1k0ua1
A:190-352
2b
d1k0ug1
G:190-352
2c
d1k0uh1
H:190-352
2d
d1k0ub1
B:190-352
2e
d1k0uc1
C:190-352
2f
d1k0ud1
D:190-352
2g
d1k0ue1
E:190-352
2h
d1k0uf1
F:190-352
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1k0uA01 (A:2-191,A:352-403)
1b: CATH_1k0uB01 (B:2-191,B:352-403)
1c: CATH_1k0uC01 (C:2-191,C:352-403)
1d: CATH_1k0uD01 (D:2-191,D:352-403)
1e: CATH_1k0uE01 (E:2-191,E:352-403)
1f: CATH_1k0uF01 (F:2-191,F:352-403)
1g: CATH_1k0uG01 (G:2-191,G:352-403)
1h: CATH_1k0uH01 (H:2-191,H:352-403)
2a: CATH_1k0uA02 (A:192-351)
2b: CATH_1k0uB02 (B:192-351)
2c: CATH_1k0uC02 (C:192-351)
2d: CATH_1k0uD02 (D:192-351)
2e: CATH_1k0uE02 (E:192-351)
2f: CATH_1k0uF02 (F:192-351)
2g: CATH_1k0uG02 (G:192-351)
2h: CATH_1k0uH02 (H:192-351)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1480, no name defined]
(11)
Norway rat (Rattus norvegicus)
(7)
1a
1k0uA01
A:2-191,A:352-403
1b
1k0uB01
B:2-191,B:352-403
1c
1k0uC01
C:2-191,C:352-403
1d
1k0uD01
D:2-191,D:352-403
1e
1k0uE01
E:2-191,E:352-403
1f
1k0uF01
F:2-191,F:352-403
1g
1k0uG01
G:2-191,G:352-403
1h
1k0uH01
H:2-191,H:352-403
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Norway rat (Rattus norvegicus)
(18)
2a
1k0uA02
A:192-351
2b
1k0uB02
B:192-351
2c
1k0uC02
C:192-351
2d
1k0uD02
D:192-351
2e
1k0uE02
E:192-351
2f
1k0uF02
F:192-351
2g
1k0uG02
G:192-351
2h
1k0uH02
H:192-351
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (531 KB)
Header - Asym.Unit
Biol.Unit 1 (268 KB)
Header - Biol.Unit 1
Biol.Unit 2 (264 KB)
Header - Biol.Unit 2
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
1K0U
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
