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.
1KEV
Biol. Unit 1
Info
Asym.Unit (236 KB)
Biol.Unit 1 (231 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 NADP-DEPENDENT ALCOHOL DEHYDROGENASE
Authors
:
Y. Korkhin, F. Frolow
Date
:
21 Oct 96 (Deposition) - 22 Oct 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Zinc, Nadp
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Korkhin, F. Frolow, O. Bogin, M. Peretz, A. J. Kalb, Y. Burstein
Crystalline Alcohol Dehydrogenases From The Mesophilic Bacterium Clostridium Beijerinckii And The Thermophilic Bacterium Thermoanaerobium Brockii: Preparation, Characterization And Molecular Symmetry.
Acta Crystallogr. , Sect. D V. 52 882 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
1b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
1c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
1d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(12, 12)
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: S1 (UNKNOWN)
10: S2 (UNKNOWN)
11: S3 (UNKNOWN)
12: S4 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:37 , SER A:39 , HIS A:59 , GLU A:60 , ASP A:150 , NDP A:352
BINDING SITE FOR RESIDUE ZN A 353
02
AC2
SOFTWARE
CYS B:37 , HIS B:59 , GLU B:60 , ASP B:150 , NDP B:352
BINDING SITE FOR RESIDUE ZN B 353
03
AC3
SOFTWARE
CYS C:37 , SER C:39 , HIS C:59 , ASP C:150 , NDP C:352
BINDING SITE FOR RESIDUE ZN C 353
04
AC4
SOFTWARE
CYS D:37 , SER D:39 , HIS D:59 , ASP D:150 , NDP D:352
BINDING SITE FOR RESIDUE ZN D 353
05
AC5
SOFTWARE
THR A:38 , SER A:39 , HIS A:42 , ASP A:150 , MET A:151 , ILE A:173 , ILE A:175 , GLY A:176 , VAL A:178 , SER A:199 , ARG A:200 , TYR A:218 , ALA A:242 , GLY A:244 , GLU A:247 , ILE A:265 , ASN A:266 , TYR A:267 , LYS A:340 , ZN A:353 , HOH A:358 , HOH A:400
BINDING SITE FOR RESIDUE NDP A 352
06
AC6
SOFTWARE
THR B:38 , ASP B:150 , ILE B:173 , GLY B:174 , ILE B:175 , GLY B:176 , ALA B:177 , VAL B:178 , SER B:199 , ARG B:200 , TYR B:218 , ALA B:242 , GLY B:244 , ILE B:265 , ASN B:266 , TYR B:267 , ZN B:353 , HOH B:365
BINDING SITE FOR RESIDUE NDP B 352
07
AC7
SOFTWARE
THR C:38 , SER C:39 , ASP C:150 , MET C:151 , ILE C:173 , GLY C:174 , ILE C:175 , GLY C:176 , ALA C:177 , VAL C:178 , SER C:199 , ARG C:200 , TYR C:218 , ALA C:242 , GLY C:243 , ILE C:265 , ASN C:266 , TYR C:267 , LYS C:340 , ZN C:353 , HOH C:366
BINDING SITE FOR RESIDUE NDP C 352
08
AC8
SOFTWARE
THR D:38 , SER D:39 , ASP D:150 , MET D:151 , ILE D:173 , GLY D:174 , ILE D:175 , GLY D:176 , ALA D:177 , VAL D:178 , SER D:199 , ARG D:200 , TYR D:218 , ALA D:242 , GLY D:243 , GLY D:244 , ILE D:265 , ASN D:266 , TYR D:267 , LYS D:340 , ZN D:353 , HOH D:373 , HOH D:417 , HOH D:493
BINDING SITE FOR RESIDUE NDP D 352
09
S1
UNKNOWN
CYS A:37 , HIS A:59 , ASP A:150 , ZN A:353
CATALYTIC SITE.
10
S2
UNKNOWN
CYS B:37 , HIS B:59 , ASP B:150 , ZN B:353
CATALYTIC SITE.
11
S3
UNKNOWN
CYS C:37 , HIS C:59 , ASP C:150 , ZN C:353
CATALYTIC SITE.
12
S4
UNKNOWN
CYS D:37 , HIS D:59 , ASP D:150 , ZN D:353
CATALYTIC SITE.
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ADH_ZINC (A:58-72,B:58-72,C:58-72,D:58-72)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_ZINC
PS00059
Zinc-containing alcohol dehydrogenases signature.
ADH_CLOBE
58-72
4
A:58-72
B:58-72
C:58-72
D:58-72
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d1keva1 (A:1-139,A:314-351)
1b: SCOP_d1kevb1 (B:1-139,B:314-351)
1c: SCOP_d1kevc1 (C:1-139,C:314-351)
1d: SCOP_d1kevd1 (D:1-139,D:314-351)
2a: SCOP_d1keva2 (A:140-313)
2b: SCOP_d1kevb2 (B:140-313)
2c: SCOP_d1kevc2 (C:140-313)
2d: SCOP_d1kevd2 (D:140-313)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Bacterial secondary alcohol dehydrogenase
(7)
Clostridium beijerinckii [TaxId: 1520]
(4)
1a
d1keva1
A:1-139,A:314-351
1b
d1kevb1
B:1-139,B:314-351
1c
d1kevc1
C:1-139,C:314-351
1d
d1kevd1
D:1-139,D:314-351
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Alcohol dehydrogenase-like, C-terminal domain
(115)
Protein domain
:
Bacterial secondary alcohol dehydrogenase
(7)
Clostridium beijerinckii [TaxId: 1520]
(4)
2a
d1keva2
A:140-313
2b
d1kevb2
B:140-313
2c
d1kevc2
C:140-313
2d
d1kevd2
D:140-313
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1kevA02 (A:155-292)
1b: CATH_1kevB02 (B:155-292)
1c: CATH_1kevC02 (C:155-292)
1d: CATH_1kevD02 (D:155-292)
2a: CATH_1kevA01 (A:1-154,A:293-351)
2b: CATH_1kevB01 (B:1-154,B:293-351)
2c: CATH_1kevC01 (C:1-154,C:293-351)
2d: CATH_1kevD01 (D:1-154,D:293-351)
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
:
NAD(P)-binding Rossmann-like Domain
(1244)
Clostridium beijerinckii. Organism_taxid: 1520.
(4)
1a
1kevA02
A:155-292
1b
1kevB02
B:155-292
1c
1kevC02
C:155-292
1d
1kevD02
D:155-292
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Clostridium beijerinckii. Organism_taxid: 1520.
(4)
2a
1kevA01
A:1-154,A:293-351
2b
1kevB01
B:1-154,B:293-351
2c
1kevC01
C:1-154,C:293-351
2d
1kevD01
D:1-154,D:293-351
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_ADH_N_1kevD01 (D:24-134)
1b: PFAM_ADH_N_1kevD02 (D:24-134)
1c: PFAM_ADH_N_1kevD03 (D:24-134)
1d: PFAM_ADH_N_1kevD04 (D:24-134)
2a: PFAM_ADH_zinc_N_1kevD05 (D:177-309)
2b: PFAM_ADH_zinc_N_1kevD06 (D:177-309)
2c: PFAM_ADH_zinc_N_1kevD07 (D:177-309)
2d: PFAM_ADH_zinc_N_1kevD08 (D:177-309)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Clostridium beijerinckii (Clostridium MP)
(3)
1a
ADH_N-1kevD01
D:24-134
1b
ADH_N-1kevD02
D:24-134
1c
ADH_N-1kevD03
D:24-134
1d
ADH_N-1kevD04
D:24-134
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Clostridium beijerinckii (Clostridium MP)
(3)
2a
ADH_zinc_N-1kevD05
D:177-309
2b
ADH_zinc_N-1kevD06
D:177-309
2c
ADH_zinc_N-1kevD07
D:177-309
2d
ADH_zinc_N-1kevD08
D:177-309
[
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 (236 KB)
Header - Asym.Unit
Biol.Unit 1 (231 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
1KEV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
