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.
1R3N
Biol. Unit 1
Info
Asym.Unit (546 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (142 KB)
Biol.Unit 3 (140 KB)
Biol.Unit 4 (139 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF BETA-ALANINE SYNTHASE FROM SACCHAROMYCES KLUYVERI
Authors
:
S. Lundgren, Z. Gojkovic, J. Piskur, D. Dobritzsch
Date
:
02 Oct 03 (Deposition) - 11 Nov 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Alpha And Beta Protein, Di-Zinc Center, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Lundgren, Z. Gojkovic, J. Piskur, D. Dobritzsch
Yeast Beta-Alanine Synthase Shares A Structural Scaffold And Origin With Dizinc-Dependent Exopeptidases
J. Biol. Chem. V. 278 51851 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: BETA-AMINO ISOBUTYRATE (BIBa)
1b: BETA-AMINO ISOBUTYRATE (BIBb)
1c: BETA-AMINO ISOBUTYRATE (BIBc)
1d: BETA-AMINO ISOBUTYRATE (BIBd)
1e: BETA-AMINO ISOBUTYRATE (BIBe)
1f: BETA-AMINO ISOBUTYRATE (BIBf)
1g: BETA-AMINO ISOBUTYRATE (BIBg)
1h: BETA-AMINO ISOBUTYRATE (BIBh)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
2m: ZINC ION (ZNm)
2n: ZINC ION (ZNn)
2o: ZINC ION (ZNo)
2p: ZINC ION (ZNp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BIB
2
Ligand/Ion
BETA-AMINO ISOBUTYRATE
2
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: BC8 (SOFTWARE)
6: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:114 , ASP A:125 , HIS A:226 , ZN A:501 , HOH A:2503 , HOH A:2504
BINDING SITE FOR RESIDUE ZN A 500
2
AC2
SOFTWARE
ASP A:125 , GLU A:160 , GLN A:229 , HIS A:421 , ZN A:500 , HOH A:2503
BINDING SITE FOR RESIDUE ZN A 501
3
AC3
SOFTWARE
HIS B:114 , ASP B:125 , GLU B:159 , HIS B:226 , ZN B:501 , HOH B:1503 , HOH B:1506
BINDING SITE FOR RESIDUE ZN B 500
4
AC4
SOFTWARE
ASP B:125 , GLU B:160 , GLN B:229 , HIS B:421 , ZN B:500 , HOH B:1506
BINDING SITE FOR RESIDUE ZN B 501
5
BC8
SOFTWARE
TRP A:251 , ARG A:322 , GLY A:396 , HOH A:2508 , HIS B:262 , ASN B:309
BINDING SITE FOR RESIDUE BIB B 1502
6
BC9
SOFTWARE
HIS A:262 , ASN A:309 , TYR B:249 , ARG B:322 , GLY B:396
BINDING SITE FOR RESIDUE BIB A 2502
[
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
(, 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, 16)
Info
All SCOP Domains
1a: SCOP_d1r3na2 (A:248-363)
1b: SCOP_d1r3nb2 (B:248-363)
1c: SCOP_d1r3nc2 (C:248-363)
1d: SCOP_d1r3nd2 (D:248-363)
1e: SCOP_d1r3ne2 (E:248-363)
1f: SCOP_d1r3nf2 (F:248-363)
1g: SCOP_d1r3ng2 (G:248-363)
1h: SCOP_d1r3nh2 (H:248-363)
2a: SCOP_d1r3na1 (A:18-247,A:364-455)
2b: SCOP_d1r3nb1 (B:23-247,B:364-455)
2c: SCOP_d1r3nc1 (C:18-247,C:364-455)
2d: SCOP_d1r3nd1 (D:19-247,D:364-455)
2e: SCOP_d1r3ne1 (E:23-247,E:364-455)
2f: SCOP_d1r3nf1 (F:18-247,F:364-455)
2g: SCOP_d1r3ng1 (G:26-247,G:364-455)
2h: SCOP_d1r3nh1 (H:18-247,H:364-455)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Bacterial exopeptidase dimerisation domain
(12)
Family
:
Bacterial exopeptidase dimerisation domain
(12)
Protein domain
:
Peptidase-like beta-alanine synthase
(2)
Yeast (Saccharomyces kluyveri) [TaxId: 4934]
(2)
1a
d1r3na2
A:248-363
1b
d1r3nb2
B:248-363
1c
d1r3nc2
C:248-363
1d
d1r3nd2
D:248-363
1e
d1r3ne2
E:248-363
1f
d1r3nf2
F:248-363
1g
d1r3ng2
G:248-363
1h
d1r3nh2
H:248-363
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
Bacterial dinuclear zinc exopeptidases
(55)
Protein domain
:
Peptidase-like beta-alanine synthase, catalytic domain
(2)
Yeast (Saccharomyces kluyveri) [TaxId: 4934]
(2)
2a
d1r3na1
A:18-247,A:364-455
2b
d1r3nb1
B:23-247,B:364-455
2c
d1r3nc1
C:18-247,C:364-455
2d
d1r3nd1
D:19-247,D:364-455
2e
d1r3ne1
E:23-247,E:364-455
2f
d1r3nf1
F:18-247,F:364-455
2g
d1r3ng1
G:26-247,G:364-455
2h
d1r3nh1
H:18-247,H:364-455
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1r3nB02 (B:248-363)
1b: CATH_1r3nC02 (C:248-363)
1c: CATH_1r3nD02 (D:248-363)
1d: CATH_1r3nE02 (E:248-363)
1e: CATH_1r3nF02 (F:248-363)
1f: CATH_1r3nG02 (G:248-363)
1g: CATH_1r3nH02 (H:248-363)
1h: CATH_1r3nA02 (A:248-363)
2a: CATH_1r3nG01 (G:26-247,G:364-455)
2b: CATH_1r3nB01 (B:23-247,B:364-455)
2c: CATH_1r3nE01 (E:23-247,E:364-455)
2d: CATH_1r3nD01 (D:19-247,D:364-455)
2e: CATH_1r3nA01 (A:18-247,A:364-455)
2f: CATH_1r3nC01 (C:18-247,C:364-455)
2g: CATH_1r3nF01 (F:18-247,F:364-455)
2h: CATH_1r3nH01 (H:18-247,H:364-455)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.360, no name defined]
(23)
Lachancea kluyveri. Organism_taxid: 4934.
(2)
1a
1r3nB02
B:248-363
1b
1r3nC02
C:248-363
1c
1r3nD02
D:248-363
1d
1r3nE02
E:248-363
1e
1r3nF02
F:248-363
1f
1r3nG02
G:248-363
1g
1r3nH02
H:248-363
1h
1r3nA02
A:248-363
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aminopeptidase
(284)
Homologous Superfamily
:
Zn peptidases
(137)
Lachancea kluyveri. Organism_taxid: 4934.
(2)
2a
1r3nG01
G:26-247,G:364-455
2b
1r3nB01
B:23-247,B:364-455
2c
1r3nE01
E:23-247,E:364-455
2d
1r3nD01
D:19-247,D:364-455
2e
1r3nA01
A:18-247,A:364-455
2f
1r3nC01
C:18-247,C:364-455
2g
1r3nF01
F:18-247,F:364-455
2h
1r3nH01
H:18-247,H:364-455
[
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
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 (546 KB)
Header - Asym.Unit
Biol.Unit 1 (142 KB)
Header - Biol.Unit 1
Biol.Unit 2 (142 KB)
Header - Biol.Unit 2
Biol.Unit 3 (140 KB)
Header - Biol.Unit 3
Biol.Unit 4 (139 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
1R3N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help