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.
1MKN
Asym. Unit
Info
Asym.Unit (18 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
N-TERMINAL HALF OF MIDKINE
Authors
:
W. Iwasaki, K. Nagata, H. Hatanaka, K. Ogura, T. Inui, T. Kimura, T. Muramatsu, K. Yoshida, M. Tasumi, F. Inagaki
Date
:
16 Mar 99 (Deposition) - 23 Mar 99 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A
Keywords
:
Heparin-Binding Growth Factor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Iwasaki, K. Nagata, H. Hatanaka, T. Inui, T. Kimura, T. Muramatsu, K. Yoshida, M. Tasumi, F. Inagaki
Solution Structure Of Midkine, A New Heparin-Binding Growth Factor.
Embo J. V. 16 6936 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PTN_MK_1 (A:13-37)
2: PTN_MK_2 (A:48-59)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PTN_MK_1
PS00619
PTN/MK heparin-binding protein family signature 1.
MK_HUMAN
35-59
1
A:13-37
2
PTN_MK_2
PS00620
PTN/MK heparin-binding protein family signature 2.
MK_HUMAN
70-94
1
A:48-59
[
close PROSITE info
]
Exons
(2, 2)
Info
All Exons
Exon 1.2i (A:1-4)
Exon 1.3c (A:4-59)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2b/1.2i
2: Boundary 1.2i/1.3c
3: Boundary 1.3c/1.4b
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2b
ENST00000395566
2b
ENSE00001890528
chr11:
46403226-46403308
83
MK_HUMAN
-
0
0
-
-
1.2i
ENST00000395566
2i
ENSE00002141825
chr11:
46403607-46403683
77
MK_HUMAN
1-26
26
1
A:1-4
4
1.3c
ENST00000395566
3c
ENSE00000712415
chr11:
46403844-46404011
168
MK_HUMAN
26-82
57
1
A:4-59
56
1.4b
ENST00000395566
4b
ENSE00001181863
chr11:
46404137-46404298
162
MK_HUMAN
82-136
55
0
-
-
1.5d
ENST00000395566
5d
ENSE00001875238
chr11:
46405019-46405356
338
MK_HUMAN
136-143
8
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1mkna_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Midkine
(2)
Superfamily
:
Midkine
(2)
Family
:
Midkine, a heparin-binding growth factor, N-terminal domain
(1)
Protein domain
:
Midkine, a heparin-binding growth factor, N-terminal domain
(1)
Synthetic
(1)
1a
d1mkna_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1mknA00 (A:1-59)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Single Sheet
(341)
Topology
:
Heparin-binding Growth Factor, Midkine; Chain A
(1)
Homologous Superfamily
:
Heparin-binding Growth Factor, Midkine; Chain A
(1)
[unclassified]
(1)
1a
1mknA00
A:1-59
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PTN_MK_N_1mknA01 (A:2-58)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: PTN_MK_N]
(1)
Family
:
PTN_MK_N
(1)
Homo sapiens (Human)
(1)
1a
PTN_MK_N-1mknA01
A:2-58
[
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
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 (18 KB)
Header - Asym.Unit
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
1MKN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
