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.
PLEASE WAIT...
Getting 'Exon' information from database.
4B2D
Asym. Unit
Info
Asym.Unit (693 KB)
Biol.Unit 1 (682 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN PKM2 WITH L-SERINE AND FBP BOUND.
Authors
:
B. Chaneton, P. Hillmann, L. Zheng, A. C. L. Martin, O. D. K. Maddocks, A. Chokkathukalam, J. E. Coyle, A. Jankevics, F. P. Holding, K. H. Vous C. Frezza, M. Oreilly, E. Gottlieb
Date
:
13 Jul 12 (Deposition) - 10 Oct 12 (Release) - 06 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transferase, Tumour, Pkm2, Glycolysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Chaneton, P. Hillmann, L. Zheng, A. C. L. Martin, O. D. K. Maddocks, A. Chokkathukalam, J. E. Coyle, A. Jankevics, F. P. Holding, K. H. Vousden, C. Frezza, M. Oreilly, E. Gottlieb
Serine Is A Natural Ligand And Allosteric Activator Of Pyruvate Kinase M2
Nature V. 491 458 2012
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPa)
1b: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPb)
1c: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPc)
1d: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: SERINE (SERa)
3b: SERINE (SERb)
3c: SERINE (SERc)
3d: SERINE (SERd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FBP
4
Ligand/Ion
BETA-FRUCTOSE-1,6-DIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
SER
4
Mod. Amino Acid
SERINE
[
close Hetero Component info
]
Sites
(10, 10)
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: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:431 , THR A:432 , LYS A:433 , SER A:434 , SER A:437 , TRP A:482 , ARG A:489 , GLY A:514 , ARG A:516 , PRO A:517 , GLY A:518 , SER A:519 , GLY A:520 , PHE A:521 , THR A:522 , HOH A:2336 , HOH A:2338 , HOH A:2344 , HOH A:2348 , HOH A:2351
BINDING SITE FOR RESIDUE FBP A 600
02
AC2
SOFTWARE
GLU A:223 , LEU B:431 , THR B:432 , LYS B:433 , SER B:434 , SER B:437 , TRP B:482 , ARG B:489 , GLY B:514 , ARG B:516 , PRO B:517 , GLY B:518 , SER B:519 , GLY B:520 , PHE B:521 , THR B:522 , HOH B:2209 , HOH B:2217 , HOH B:2218 , HOH B:2223 , HOH B:2241
BINDING SITE FOR RESIDUE FBP B 600
03
AC3
SOFTWARE
LEU C:431 , THR C:432 , LYS C:433 , SER C:434 , ARG C:436 , SER C:437 , TRP C:482 , ARG C:489 , GLY C:514 , ARG C:516 , PRO C:517 , GLY C:518 , SER C:519 , GLY C:520 , PHE C:521 , THR C:522 , HOH C:2281 , HOH C:2282 , HOH C:2286 , HOH C:2289
BINDING SITE FOR RESIDUE FBP C 600
04
AC4
SOFTWARE
THR D:432 , LYS D:433 , SER D:434 , SER D:437 , TRP D:482 , ARG D:489 , GLY D:514 , ARG D:516 , PRO D:517 , GLY D:518 , SER D:519 , GLY D:520 , PHE D:521 , THR D:522 , HOH D:2195 , HOH D:2204 , HOH D:2205 , HOH D:2248
BINDING SITE FOR RESIDUE FBP D 600
05
AC5
SOFTWARE
GLU A:272 , ASP A:296 , HOH A:2237
BINDING SITE FOR RESIDUE MG A 700
06
AC6
SOFTWARE
GLU C:272 , ASP C:296 , HOH C:2190
BINDING SITE FOR RESIDUE MG C 700
07
AC7
SOFTWARE
ARG D:43 , ASN D:44 , ASN D:70 , ARG D:106 , HIS D:464 , ILE D:469 , PHE D:470 , PRO D:471 , HOH D:2028 , HOH D:2029 , HOH D:2036 , HOH D:2057
BINDING SITE FOR RESIDUE SER D1532
08
AC8
SOFTWARE
ARG A:43 , ASN A:44 , ASN A:70 , ARG A:106 , HIS A:464 , ILE A:469 , PHE A:470 , PRO A:471 , HOH A:2038 , HOH A:2039 , HOH A:2045
BINDING SITE FOR RESIDUE SER A1532
09
AC9
SOFTWARE
ARG B:43 , ASN B:70 , ARG B:106 , HIS B:464 , ILE B:469 , PHE B:470 , PRO B:471 , HOH B:2029 , HOH B:2030 , HOH B:2032 , HOH B:2089
BINDING SITE FOR RESIDUE SER B1532
10
BC1
SOFTWARE
ARG C:43 , ASN C:44 , ASN C:70 , ARG C:106 , HIS C:464 , ILE C:469 , PHE C:470 , PRO C:471 , HOH C:2034 , HOH C:2035 , HOH C:2037 , HOH C:2057
BINDING SITE FOR RESIDUE SER C1532
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_033067 (G204V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_033067
G
204
V
KPYM_HUMAN
Polymorphism
17853396
A/B/C/D
G
204
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PYRUVATE_KINASE (A:265-277,B:265-277,C:265-277,D:26...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRUVATE_KINASE
PS00110
Pyruvate kinase active site signature.
KPYM_HUMAN
265-277
4
A:265-277
B:265-277
C:265-277
D:265-277
[
close PROSITE info
]
Exons
(10, 40)
Info
All Exons
Exon 1.3a (A:14-52 | B:14-52 | C:14-52 | D:14...)
Exon 1.4b (A:52-82 | B:52-82 | C:52-82 | D:52...)
Exon 1.5b (A:83-126 | B:83-125 | C:83-126 | D...)
Exon 1.6a (A:127-189 | B:130-189 | C:127-189 ...)
Exon 1.7a (A:189-279 | B:189-279 | C:189-279 ...)
Exon 1.8 (A:279-329 | B:279-329 | C:279-329 ...)
Exon 1.9 (A:330-380 | B:330-380 | C:330-380 ...)
Exon 1.11 (A:381-436 | B:381-436 | C:381-436 ...)
Exon 1.12 (A:436-497 | B:436-497 | C:436-497 ...)
Exon 1.13b (A:497-531 | B:497-531 | C:497-531 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.3a
02: Boundary 1.3a/1.4b
03: Boundary 1.4b/1.5b
04: Boundary 1.5b/1.6a
05: Boundary 1.6a/1.7a
06: Boundary 1.7a/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13b
11: Boundary 1.13b/-
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
1.1a
ENST00000335181
1a
ENSE00001360078
chr15:
72523684-72523457
228
KPYM_HUMAN
-
0
0
-
-
1.3a
ENST00000335181
3a
ENSE00001730487
chr15:
72511451-72511285
167
KPYM_HUMAN
1-52
52
4
A:14-52
B:14-52
C:14-52
D:14-52
39
39
39
39
1.4b
ENST00000335181
4b
ENSE00000374128
chr15:
72509841-72509750
92
KPYM_HUMAN
52-82
31
4
A:52-82
B:52-82
C:52-82
D:52-82
31
31
31
31
1.5b
ENST00000335181
5b
ENSE00000943411
chr15:
72502819-72502688
132
KPYM_HUMAN
83-126
44
4
A:83-126
B:83-125
C:83-126
D:83-126
44
43
44
44
1.6a
ENST00000335181
6a
ENSE00000943412
chr15:
72502200-72502014
187
KPYM_HUMAN
127-189
63
4
A:127-189
B:130-189
C:127-189
D:127-189
63
60
63
63
1.7a
ENST00000335181
7a
ENSE00001504881
chr15:
72501232-72500962
271
KPYM_HUMAN
189-279
91
4
A:189-279
B:189-279
C:189-279
D:189-279
91
91
91
91
1.8
ENST00000335181
8
ENSE00001179435
chr15:
72499618-72499468
151
KPYM_HUMAN
279-329
51
4
A:279-329
B:279-329
C:279-329
D:279-329
51
51
51
51
1.9
ENST00000335181
9
ENSE00001220626
chr15:
72499221-72499069
153
KPYM_HUMAN
330-380
51
4
A:330-380
B:330-380
C:330-380
D:330-380
51
51
51
51
1.11
ENST00000335181
11
ENSE00001220667
chr15:
72494961-72494795
167
KPYM_HUMAN
381-436
56
4
A:381-436
B:381-436
C:381-436
D:381-436
56
56
56
56
1.12
ENST00000335181
12
ENSE00001220742
chr15:
72492996-72492815
182
KPYM_HUMAN
436-497
62
4
A:436-497
B:436-497
C:436-497
D:436-497
62
62
62
62
1.13b
ENST00000335181
13b
ENSE00001179472
chr15:
72492097-72491370
728
KPYM_HUMAN
497-531
35
4
A:497-531
B:497-531
C:497-531
D:497-531
35
35
35
35
[
close EXON info
]
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 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 (693 KB)
Header - Asym.Unit
Biol.Unit 1 (682 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
4B2D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help