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.
1BHN
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (161 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA
Authors
:
J. E. Ladner, N. G. Abdulaev, D. L. Kakuev, G. N. Karaschuk, M. Tordova, E. Eisenstein, J. H. Fujiwara, K. D. Ridge, G. L. Gilliland
Date
:
10 Jun 98 (Deposition) - 16 Feb 99 (Release) - 15 Sep 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Phosphotransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. E. Ladner, N. G. Abdulaev, D. L. Kakuev, M. Tordova, K. D. Ridge, G. L. Gilliland
The Three-Dimensional Structures Of Two Isoforms Of Nucleoside Diphosphate Kinase From Bovine Retina.
Acta Crystallogr. , Sect. D V. 55 1127 1999
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: GUANOSINE-3',5'-MONOPHOSPHATE (35Ga)
1b: GUANOSINE-3',5'-MONOPHOSPHATE (35Gb)
1c: GUANOSINE-3',5'-MONOPHOSPHATE (35Gc)
1d: GUANOSINE-3',5'-MONOPHOSPHATE (35Gd)
1e: GUANOSINE-3',5'-MONOPHOSPHATE (35Ge)
1f: GUANOSINE-3',5'-MONOPHOSPHATE (35Gf)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
2c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
2d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
2e: GUANOSINE-5'-DIPHOSPHATE (GDPe)
2f: GUANOSINE-5'-DIPHOSPHATE (GDPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
35G
6
Ligand/Ion
GUANOSINE-3',5'-MONOPHOSPHATE
2
GDP
6
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: A (UNKNOWN)
02: AC1 (SOFTWARE)
03: AC2 (SOFTWARE)
04: AC3 (SOFTWARE)
05: AC4 (SOFTWARE)
06: AC5 (SOFTWARE)
07: AC6 (SOFTWARE)
08: AC7 (SOFTWARE)
09: AC8 (SOFTWARE)
10: AC9 (SOFTWARE)
11: B (UNKNOWN)
12: BC1 (SOFTWARE)
13: BC2 (SOFTWARE)
14: BC3 (SOFTWARE)
15: C (UNKNOWN)
16: D (UNKNOWN)
17: E (UNKNOWN)
18: F (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
A
UNKNOWN
LYS A:12 , TYR A:52 , VAL A:112 , ASN A:115 , HIS A:118 , GLU A:152
C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.
02
AC1
SOFTWARE
LYS A:12 , TYR A:52 , PHE A:60 , ARG A:105 , VAL A:112 , ASN A:115 , HIS A:118 , GDP A:161 , HOH A:502
BINDING SITE FOR RESIDUE 35G A 160
03
AC2
SOFTWARE
LYS A:12 , PHE A:60 , ARG A:88 , THR A:94 , ARG A:105 , VAL A:112 , GLY A:113 , ASN A:115 , HIS A:118 , 35G A:160 , HOH A:502 , GLU B:152
BINDING SITE FOR RESIDUE GDP A 161
04
AC3
SOFTWARE
LYS B:12 , TYR B:52 , PHE B:60 , ARG B:105 , VAL B:112 , ASN B:115 , HIS B:118 , GDP B:161 , HOH B:372 , HOH B:503 , GLU C:152
BINDING SITE FOR RESIDUE 35G B 160
05
AC4
SOFTWARE
LYS B:12 , TYR B:52 , LEU B:55 , PHE B:60 , LEU B:64 , ARG B:88 , VAL B:112 , ASN B:115 , HIS B:118 , GLY B:119 , 35G B:160 , HOH B:204 , HOH B:372 , HOH B:503 , GLU C:152
BINDING SITE FOR RESIDUE GDP B 161
06
AC5
SOFTWARE
LYS C:12 , TYR C:52 , PHE C:60 , LEU C:64 , THR C:94 , ASN C:115 , HIS C:118 , GDP C:161 , HOH C:238 , HOH C:505
BINDING SITE FOR RESIDUE 35G C 160
07
AC6
SOFTWARE
GLU A:152 , LYS C:12 , PHE C:60 , LEU C:64 , ARG C:88 , THR C:94 , ARG C:105 , VAL C:112 , ASN C:115 , 35G C:160 , HOH C:497 , HOH C:505
BINDING SITE FOR RESIDUE GDP C 161
08
AC7
SOFTWARE
LYS D:12 , TYR D:52 , PHE D:60 , LEU D:64 , VAL D:112 , GLY D:113 , ASN D:115 , HIS D:118 , GDP D:161
BINDING SITE FOR RESIDUE 35G D 160
09
AC8
SOFTWARE
LYS D:12 , LEU D:55 , PHE D:60 , LEU D:64 , ARG D:88 , THR D:94 , ARG D:105 , VAL D:112 , ASN D:115 , 35G D:160 , HOH D:285 , HOH D:507
BINDING SITE FOR RESIDUE GDP D 161
10
AC9
SOFTWARE
LYS E:12 , PHE E:60 , THR E:94 , ASN E:115 , HIS E:118 , GDP E:161 , HOH E:221 , GLU F:152
BINDING SITE FOR RESIDUE 35G E 160
11
B
UNKNOWN
LYS B:12 , TYR B:52 , VAL B:112 , ASN B:115 , HIS B:118 , GLU B:152
C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.
12
BC1
SOFTWARE
LYS E:12 , PHE E:60 , LEU E:64 , ARG E:88 , THR E:94 , VAL E:112 , ASN E:115 , 35G E:160 , HOH E:221 , HOH E:266 , GLU F:152
BINDING SITE FOR RESIDUE GDP E 161
13
BC2
SOFTWARE
GLU D:152 , LYS F:12 , TYR F:52 , PHE F:60 , ARG F:105 , VAL F:112 , GLY F:113 , ASN F:115 , HIS F:118 , GDP F:161 , HOH F:377 , HOH F:494
BINDING SITE FOR RESIDUE 35G F 160
14
BC3
SOFTWARE
GLU D:152 , LYS F:12 , LEU F:55 , PHE F:60 , LEU F:64 , ARG F:88 , THR F:94 , VAL F:112 , ASN F:115 , HIS F:118 , 35G F:160 , HOH F:377 , HOH F:494 , HOH F:495
BINDING SITE FOR RESIDUE GDP F 161
15
C
UNKNOWN
LYS C:12 , TYR C:52 , VAL C:112 , ASN C:115 , HIS C:118 , GLU C:152
C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.
16
D
UNKNOWN
LYS D:12 , TYR D:52 , VAL D:112 , ASN D:115 , HIS D:118 , GLU D:152
C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.
17
E
UNKNOWN
LYS E:12 , TYR E:52 , VAL E:112 , ASN E:115 , HIS E:118 , GLU E:152
C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.
18
F
UNKNOWN
LYS F:12 , TYR F:52 , VAL F:112 , ASN F:115 , HIS F:118 , GLU F:152
C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.
[
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
(1, 6)
Info
All PROSITE Patterns/Profiles
1: NDP_KINASES (A:115-123,B:115-123,C:115-123,D:11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NDP_KINASES
PS00469
Nucleoside diphosphate kinases active site.
NDKA1_BOVIN
115-123
6
A:115-123
B:115-123
C:115-123
D:115-123
E:115-123
F:115-123
[
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1bhna_ (A:)
1b: SCOP_d1bhnb_ (B:)
1c: SCOP_d1bhnc_ (C:)
1d: SCOP_d1bhnd_ (D:)
1e: SCOP_d1bhne_ (E:)
1f: SCOP_d1bhnf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Nucleoside diphosphate kinase, NDK
(129)
Family
:
Nucleoside diphosphate kinase, NDK
(112)
Protein domain
:
Nucleoside diphosphate kinase, NDK
(66)
Cow (Bos taurus) [TaxId: 9913]
(2)
1a
d1bhna_
A:
1b
d1bhnb_
B:
1c
d1bhnc_
C:
1d
d1bhnd_
D:
1e
d1bhne_
E:
1f
d1bhnf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1bhnA00 (A:2-152)
1b: CATH_1bhnB00 (B:2-152)
1c: CATH_1bhnC00 (C:2-152)
1d: CATH_1bhnD00 (D:2-152)
1e: CATH_1bhnE00 (E:2-152)
1f: CATH_1bhnF00 (F:2-152)
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=3.30.70.141, no name defined]
(46)
Cattle (Bos taurus)
(2)
1a
1bhnA00
A:2-152
1b
1bhnB00
B:2-152
1c
1bhnC00
C:2-152
1d
1bhnD00
D:2-152
1e
1bhnE00
E:2-152
1f
1bhnF00
F:2-152
[
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
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 (168 KB)
Header - Asym.Unit
Biol.Unit 1 (161 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
1BHN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help