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...
Getting 'PROSITE' information from database.
3MKP
Biol. Unit 2
Info
Asym.Unit (127 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (62 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 1K1 MUTANT OF HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR FRAGMENT NK1 IN COMPLEX WITH HEPARIN
Authors
:
E. Gherardi, D. Y. Chirgadze, T. L. Blundell
Date
:
15 Apr 10 (Deposition) - 18 Aug 10 (Release) - 18 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.81
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Growth Factor, Supramolecular Assembly, Hgf/Sf, Met Receptor, Nk1, Hormone
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Gherardi, D. Y. Chirgadze, M. Bocci, C. Brocchieri, D. Bevan, J. Kajstura, G. Esposito, D. Lietha, M. Rota, A. Leri, N. Mallorqui-Fernandez, A. Bandyopadhyay, M. Youles, B. Mulloy, A. Rowe, M. Alison, D. Edwards, V. Vannini, T. Blundell, P. Anversa
Engineering A Fragment Of Hepatocyte Growth Factor/Scatter Factor For Tissue And Organ Regeneration
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
1c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
1d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
2a: O2-SULFO-GLUCURONIC ACID (IDSa)
2b: O2-SULFO-GLUCURONIC ACID (IDSb)
2c: O2-SULFO-GLUCURONIC ACID (IDSc)
3a: N,O6-DISULFO-GLUCOSAMINE (SGNa)
3b: N,O6-DISULFO-GLUCOSAMINE (SGNb)
3c: N,O6-DISULFO-GLUCOSAMINE (SGNc)
3d: N,O6-DISULFO-GLUCOSAMINE (SGNd)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
IDS
3
Ligand/Ion
O2-SULFO-GLUCURONIC ACID
3
SGN
3
Ligand/Ion
N,O6-DISULFO-GLUCOSAMINE
4
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC6 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC6
SOFTWARE
ARG C:168 , GLY C:169 , LYS C:170 , ASP C:171 , LEU C:172 , GLN C:173
BINDING SITE FOR RESIDUE SO4 C 3
02
AC7
SOFTWARE
PHE C:162 , GLU C:183 , GLU C:184 , GLY C:186 , TRP C:188 , ARG C:197 , TYR C:198 , GLU D:111 , PHE D:112
BINDING SITE FOR RESIDUE EPE C 211
03
AC8
SOFTWARE
SGN C:6 , IDS C:7 , ARG C:73 , ARG C:76 , LYS C:78 , GLY C:79 , IDS C:212
BINDING SITE FOR RESIDUE SGN C 2
04
AC9
SOFTWARE
SGN C:2 , SGN C:4 , IDS C:5 , SGN C:6 , IDS C:7 , LYS C:62 , ARG C:73 , GLY C:79
BINDING SITE FOR RESIDUE IDS C 212
05
BC1
SOFTWARE
IDS C:5 , SGN C:6 , LYS C:60 , THR C:61 , LYS C:62 , LYS C:63 , IDS C:212
BINDING SITE FOR RESIDUE SGN C 4
06
BC2
SOFTWARE
SGN C:4 , SGN C:6 , THR C:61 , LYS C:62 , LYS C:63 , ARG C:73 , IDS C:212
BINDING SITE FOR RESIDUE IDS C 5
07
BC3
SOFTWARE
SGN C:2 , SGN C:4 , IDS C:5 , IDS C:7 , THR C:61 , LYS C:63 , ARG C:73 , GLN C:95 , IDS C:212
BINDING SITE FOR RESIDUE SGN C 6
08
BC4
SOFTWARE
SGN C:2 , SGN C:6 , LYS C:62 , ARG C:73 , IDS C:212
BINDING SITE FOR RESIDUE IDS C 7
09
BC5
SOFTWARE
GLY D:169 , LYS D:170 , ASP D:171
BINDING SITE FOR RESIDUE SO4 D 4
10
BC6
SOFTWARE
HIS A:158 , GLU A:159 , ARG A:197 , GLU D:184 , GLY D:185 , GLY D:186 , TRP D:188 , PHE D:190 , ARG D:197 , HOH D:220 , HOH D:236
BINDING SITE FOR RESIDUE EPE D 211
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_014570 (S153I, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_014570
S
153
I
HGF_HUMAN
Polymorphism
17566
C/D
S
153
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 5)
Info
All PROSITE Patterns/Profiles
1: PAN (C:37-123)
2: KRINGLE_2 (C:127-206,D:127-206|-|-|-)
3: KRINGLE_1 (C:176-189,D:176-189|-|-|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PAN
PS50948
PAN/Apple domain profile.
HGF_HUMAN
37-123
1
-
-
C:37-123
2
KRINGLE_2
PS50070
Kringle domain profile.
HGF_HUMAN
127-206
210-288
304-383
390-469
2
-
-
C:127-206
D:127-206
-
-
-
3
KRINGLE_1
PS00021
Kringle domain signature.
HGF_HUMAN
176-189
259-271
353-365
439-452
2
-
-
C:176-189
D:176-189
-
-
-
[
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_d3mkpa1 (A:36-126)
1b: SCOP_d3mkpb1 (B:36-126)
1c: SCOP_d3mkpc1 (C:36-126)
1d: SCOP_d3mkpd1 (D:40-126)
2a: SCOP_d3mkpa2 (A:127-208)
2b: SCOP_d3mkpb2 (B:127-208)
2c: SCOP_d3mkpc2 (C:127-208)
2d: SCOP_d3mkpd2 (D:127-208)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Hairpin loop containing domain-like
(17)
Superfamily
:
Hairpin loop containing domain-like
(17)
Family
:
Hairpin loop containing domain
(15)
Protein domain
:
automated matches
(4)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d3mkpa1
A:36-126
1b
d3mkpb1
B:36-126
1c
d3mkpc1
C:36-126
1d
d3mkpd1
D:40-126
Fold
:
Kringle-like
(68)
Superfamily
:
Kringle-like
(68)
Family
:
Kringle modules
(54)
Protein domain
:
automated matches
(6)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3mkpa2
A:127-208
2b
d3mkpb2
B:127-208
2c
d3mkpc2
C:127-208
2d
d3mkpd2
D:127-208
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_PAN_1_3mkpD01 (D:40-124)
1b: PFAM_PAN_1_3mkpD02 (D:40-124)
1c: PFAM_PAN_1_3mkpD03 (D:40-124)
1d: PFAM_PAN_1_3mkpD04 (D:40-124)
2a: PFAM_Kringle_3mkpD05 (D:128-206)
2b: PFAM_Kringle_3mkpD06 (D:128-206)
2c: PFAM_Kringle_3mkpD07 (D:128-206)
2d: PFAM_Kringle_3mkpD08 (D:128-206)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PAN
(4)
Family
:
PAN_1
(4)
Homo sapiens (Human)
(3)
1a
PAN_1-3mkpD01
D:40-124
1b
PAN_1-3mkpD02
D:40-124
1c
PAN_1-3mkpD03
D:40-124
1d
PAN_1-3mkpD04
D:40-124
Clan
:
no clan defined [family: Kringle]
(26)
Family
:
Kringle
(26)
Homo sapiens (Human)
(19)
2a
Kringle-3mkpD05
D:128-206
2b
Kringle-3mkpD06
D:128-206
2c
Kringle-3mkpD07
D:128-206
2d
Kringle-3mkpD08
D:128-206
[
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 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 (127 KB)
Header - Asym.Unit
Biol.Unit 1 (61 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 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
3MKP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
