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.
4XYJ
Biol. Unit 2
Info
Asym.Unit (959 KB)
Biol.Unit 1 (483 KB)
Biol.Unit 2 (477 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 HUMAN PHOSPHOFRUCTOKINASE-1 IN COMPLEX WITH ATP AND MG, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR9275
Authors
:
F. Forouhar, B. A. Webb, F. -E. Szu, J. Seetharaman, D. L. Barber, L. Tong Northeast Structural Genomics Consortium (Nesg)
Date
:
02 Feb 15 (Deposition) - 20 May 15 (Release) - 15 Jul 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Transferase, Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. A. Webb, F. Forouhar, F. E. Szu, J. Seetharaman, L. Tong, D. L. Barber
Structures Of Human Phosphofructokinase-1 And Atomic Basis Of Cancer-Associated Mutations.
Nature V. 523 111 2015
[
close entry info
]
Hetero Components
(2, 10)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
1e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
1f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
1g: ADENOSINE-5'-TRIPHOSPHATE (ATPg)
1h: ADENOSINE-5'-TRIPHOSPHATE (ATPh)
2a: COBALT (II) ION (COa)
2b: COBALT (II) ION (COb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
3o: MAGNESIUM ION (MGo)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
4f: PHOSPHATE ION (PO4f)
4g: PHOSPHATE ION (PO4g)
4h: PHOSPHATE ION (PO4h)
4i: PHOSPHATE ION (PO4i)
4j: PHOSPHATE ION (PO4j)
4k: PHOSPHATE ION (PO4k)
4l: PHOSPHATE ION (PO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
4
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CO
-1
Ligand/Ion
COBALT (II) ION
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PO4
6
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(19, 19)
Info
All Sites
01: AE1 (SOFTWARE)
02: AE2 (SOFTWARE)
03: AE3 (SOFTWARE)
04: AE4 (SOFTWARE)
05: AE5 (SOFTWARE)
06: AE6 (SOFTWARE)
07: AE7 (SOFTWARE)
08: AE8 (SOFTWARE)
09: AE9 (SOFTWARE)
10: AF1 (SOFTWARE)
11: AF2 (SOFTWARE)
12: AF3 (SOFTWARE)
13: AF4 (SOFTWARE)
14: AF5 (SOFTWARE)
15: AF6 (SOFTWARE)
16: AF7 (SOFTWARE)
17: AF8 (SOFTWARE)
18: AF9 (SOFTWARE)
19: AG1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AE1
SOFTWARE
SER E:32 , GLY E:33 , GLY E:34 , TYR E:64 , ARG E:97 , CYS E:98 , PHE E:101 , ARG E:102 , GLY E:127 , ASP E:128 , GLY E:129 , SER E:130 , THR E:132 , GLY E:133 , SER E:173 , ASP E:175 , ARG E:219 , MG E:802 , MG E:803
binding site for residue ATP E 801
02
AE2
SOFTWARE
ASP E:128 , ASP E:177 , ATP E:801
binding site for residue MG E 802
03
AE3
SOFTWARE
SER E:32 , GLY E:34 , GLY E:127 , GLY E:172 , SER E:173 , ATP E:801
binding site for residue MG E 803
04
AE4
SOFTWARE
GLY E:233 , LYS E:264 , ARG E:430 , ARG E:434 , GLY E:467 , GLY E:468
binding site for residue PO4 E 804
05
AE5
SOFTWARE
GLY F:33 , GLY F:34 , TYR F:64 , ARG F:97 , CYS F:98 , PHE F:101 , ARG F:102 , GLY F:127 , ASP F:128 , GLY F:129 , SER F:130 , THR F:132 , GLY F:133 , SER F:173 , ASP F:175 , ASP F:177 , ARG F:219 , MG F:802 , MG F:803
binding site for residue ATP F 801
06
AE6
SOFTWARE
ASP F:128 , ASP F:177 , ARG F:219 , ATP F:801
binding site for residue MG F 802
07
AE7
SOFTWARE
SER F:32 , GLY F:34 , GLY F:127 , GLY F:172 , ATP F:801
binding site for residue MG F 803
08
AE8
SOFTWARE
ARG F:44 , ARG F:48 , SER F:83 , SER F:84
binding site for residue PO4 F 804
09
AE9
SOFTWARE
GLY F:233 , LYS F:264 , ARG F:430 , ARG F:434 , GLY F:467 , GLY F:468
binding site for residue PO4 F 805
10
AF1
SOFTWARE
HIS B:19 , GLU F:489 , LYS F:524 , HIS F:525
binding site for residue CO F 806
11
AF2
SOFTWARE
SER G:32 , GLY G:33 , GLY G:34 , TYR G:64 , ARG G:97 , CYS G:98 , PHE G:101 , ARG G:102 , GLY G:127 , ASP G:128 , GLY G:129 , SER G:130 , THR G:132 , GLY G:133 , SER G:173 , ASP G:175 , ARG G:219 , MG G:802 , MG G:803
binding site for residue ATP G 801
12
AF3
SOFTWARE
ASP G:128 , ASP G:177 , ARG G:219 , ATP G:801
binding site for residue MG G 802
13
AF4
SOFTWARE
SER G:32 , GLY G:34 , GLY G:127 , GLY G:172 , ATP G:801
binding site for residue MG G 803
14
AF5
SOFTWARE
GLY G:233 , LYS G:264 , ARG G:430 , ARG G:434 , GLY G:467 , GLY G:468
binding site for residue PO4 G 804
15
AF6
SOFTWARE
ARG G:44 , ARG G:48 , SER G:83 , SER G:84
binding site for residue PO4 G 805
16
AF7
SOFTWARE
GLY H:33 , GLY H:34 , TYR H:64 , ARG H:97 , CYS H:98 , PHE H:101 , ARG H:102 , GLY H:126 , GLY H:127 , ASP H:128 , GLY H:129 , SER H:130 , SER H:173 , ASP H:175 , ARG H:219 , MG H:802 , MG H:803
binding site for residue ATP H 801
17
AF8
SOFTWARE
ASP H:128 , ARG H:219 , ATP H:801
binding site for residue MG H 802
18
AF9
SOFTWARE
SER H:32 , GLY H:34 , GLY H:126 , GLY H:127 , GLY H:172 , SER H:173 , ATP H:801
binding site for residue MG H 803
19
AG1
SOFTWARE
GLY H:233 , ARG H:430 , ARG H:434 , GLY H:467 , GLY H:468
binding site for residue PO4 H 804
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 E
Chain F
Chain G
Chain H
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 (959 KB)
Header - Asym.Unit
Biol.Unit 1 (483 KB)
Header - Biol.Unit 1
Biol.Unit 2 (477 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
4XYJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
