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.
1EXV
Asym. Unit
Info
Asym.Unit (273 KB)
Biol.Unit 1 (267 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-403, 700
Authors
:
V. L. Rath, M. Ammirati, D. E. Danley, J. L. Ekstrom, T. R. Hynes, T. V. Ols D. J. Hoover
Date
:
04 May 00 (Deposition) - 01 Nov 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Allosteric Site, Allosteric Binding, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. L. Rath, M. Ammirati, D. E. Danley, J. L. Ekstrom, E. M. Gibbs, T. R. Hynes, A. M. Mathiowetz, R. K. Mcpherson, T. V. Olson, J. L. Treadway, D. J. Hoover
Human Liver Glycogen Phosphorylase Inhibitors Bind At A New Allosteric Site.
Chem. Biol. V. 7 677 2000
[
close entry info
]
Hetero Components
(4, 8)
Info
All Hetero Components
1a: [5-CHLORO-1H-INDOL-2-CARBONYL-PHEN... (700a)
1b: [5-CHLORO-1H-INDOL-2-CARBONYL-PHEN... (700b)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3a: 1-N-ACETYL-BETA-D-GLUCOSAMINE (NBGa)
3b: 1-N-ACETYL-BETA-D-GLUCOSAMINE (NBGb)
4a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
4b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
700
2
Ligand/Ion
[5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID
2
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NBG
2
Ligand/Ion
1-N-ACETYL-BETA-D-GLUCOSAMINE
4
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:136 , ASN A:284 , HIS A:377 , VAL A:455 , ASN A:484 , TYR A:573 , GLU A:672 , ALA A:673 , SER A:674 , GLY A:675 , HOH A:2107 , HOH A:2229 , HOH A:2280
BINDING SITE FOR RESIDUE NBG A 861
2
AC2
SOFTWARE
LEU B:136 , LEU B:139 , ASN B:284 , HIS B:377 , VAL B:455 , ASN B:484 , TYR B:573 , GLU B:672 , ALA B:673 , SER B:674 , GLY B:675 , HOH B:2212 , HOH B:2287
BINDING SITE FOR RESIDUE NBG B 1861
3
AC3
SOFTWARE
TYR A:90 , GLY A:134 , GLY A:135 , TRP A:491 , LYS A:568 , LYS A:574 , ARG A:649 , VAL A:650 , GLY A:675 , THR A:676 , GLY A:677 , LYS A:680 , HOH A:2016 , HOH A:2174 , HOH A:2278
BINDING SITE FOR RESIDUE PLP A 860
4
AC4
SOFTWARE
TRP B:491 , LYS B:568 , LYS B:574 , TYR B:648 , ARG B:649 , VAL B:650 , GLY B:675 , THR B:676 , GLY B:677 , LYS B:680 , HOH B:2006 , HOH B:2041 , HOH B:2054 , HOH B:2093 , HOH B:2246
BINDING SITE FOR RESIDUE PLP B 1860
5
AC5
SOFTWARE
ARG A:60 , LEU A:63 , TRP A:67 , PRO A:188 , GLU A:190 , LYS A:191 , HOH A:2118 , HOH A:2270 , THR B:38 , VAL B:40 , PHE B:53 , HIS B:57 , PRO B:188 , HOH B:2144
BINDING SITE FOR RESIDUE 700 A 862
6
AC6
SOFTWARE
THR A:38 , VAL A:40 , PHE A:53 , HIS A:57 , PRO A:188 , ARG B:60 , LEU B:63 , TRP B:67 , PRO B:188 , GLU B:190 , LYS B:191 , HOH B:2125 , HOH B:2141
BINDING SITE FOR RESIDUE 700 B 1862
7
AC7
SOFTWARE
TRP A:67 , ARG A:193 , VAL B:40
BINDING SITE FOR RESIDUE MPD A 1901
8
AC8
SOFTWARE
VAL A:40 , TRP B:67 , ARG B:193 , HOH B:2127
BINDING SITE FOR RESIDUE MPD B 1902
[
close Site info
]
SAPs(SNPs)/Variants
(8, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_007907 (V221I, chain A/B, )
2: VAR_013095 (V230E, chain A/B, )
3: VAR_007908 (N338S, chain A/B, )
4: VAR_007909 (N376K, chain A/B, )
5: VAR_034425 (R424P, chain A/B, )
6: VAR_034426 (V697G, chain A/B, )
7: VAR_013096 (R714S, chain A/B, )
8: VAR_034427 (I805L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_007907
V
222
I
PYGL_HUMAN
Polymorphism
946616
A/B
V
221
I
2
UniProt
VAR_013095
V
231
E
PYGL_HUMAN
Polymorphism
1042195
A/B
V
230
E
3
UniProt
VAR_007908
N
339
S
PYGL_HUMAN
Disease (GSD6)
---
A/B
N
338
S
4
UniProt
VAR_007909
N
377
K
PYGL_HUMAN
Disease (GSD6)
---
A/B
N
376
K
5
UniProt
VAR_034425
R
425
P
PYGL_HUMAN
Polymorphism
2228499
A/B
R
424
P
6
UniProt
VAR_034426
V
698
G
PYGL_HUMAN
Polymorphism
35831273
A/B
V
697
G
7
UniProt
VAR_013096
R
715
S
PYGL_HUMAN
Polymorphism
1042210
A/B
R
714
S
8
UniProt
VAR_034427
I
806
L
PYGL_HUMAN
Polymorphism
34313873
A/B
I
805
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PHOSPHORYLASE (A:672-684,B:672-684)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHORYLASE
PS00102
Phosphorylase pyridoxal-phosphate attachment site.
PYGL_HUMAN
673-685
2
A:672-684
B:672-684
[
close PROSITE info
]
Exons
(20, 40)
Info
All Exons
Exon 1.1a (A:23-80 | B:23-80)
Exon 1.2 (A:81-114 | B:81-114)
Exon 1.3b (A:115-141 | B:115-141)
Exon 1.4a (A:141-175 | B:141-175)
Exon 1.5a (A:176-219 | B:176-219)
Exon 1.6 (A:220-249 | B:220-249)
Exon 1.7 (A:260-284 | B:260-284)
Exon 1.8a (A:285-332 (gaps) | B:285-332 (gaps...)
Exon 1.9 (A:333-363 | B:333-363)
Exon 1.10a (A:364-412 | B:364-412)
Exon 1.11 (A:413-467 | B:413-467)
Exon 1.12 (A:467-505 | B:467-505)
Exon 1.13 (A:506-539 | B:506-539)
Exon 1.14a (A:540-589 | B:540-589)
Exon 1.15a (A:589-608 | B:589-608)
Exon 1.16b (A:609-656 | B:609-656)
Exon 1.17b (A:656-725 | B:656-725)
Exon 1.18 (A:725-770 | B:725-770)
Exon 1.19a (A:770-792 | B:770-792)
Exon 1.20a (A:793-830 | B:793-830)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3b
04: Boundary 1.3b/1.4a
05: Boundary 1.4a/1.5a
06: Boundary 1.5a/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8a
09: Boundary 1.8a/1.9
10: Boundary 1.9/1.10a
11: Boundary 1.10a/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14a
15: Boundary 1.14a/1.15a
16: Boundary 1.15a/1.16b
17: Boundary 1.16b/1.17b
18: Boundary 1.17b/1.18
19: Boundary 1.18/1.19a
20: Boundary 1.19a/1.20a
21: Boundary 1.20a/-
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
ENST00000216392
1a
ENSE00001368552
chr14:
51411234-51410879
356
PYGL_HUMAN
1-81
81
2
A:23-80
B:23-80
58
58
1.2
ENST00000216392
2
ENSE00000657195
chr14:
51404555-51404454
102
PYGL_HUMAN
82-115
34
2
A:81-114
B:81-114
34
34
1.3b
ENST00000216392
3b
ENSE00000657194
chr14:
51401903-51401825
79
PYGL_HUMAN
116-142
27
2
A:115-141
B:115-141
27
27
1.4a
ENST00000216392
4a
ENSE00000657193
chr14:
51398494-51398391
104
PYGL_HUMAN
142-176
35
2
A:141-175
B:141-175
35
35
1.5a
ENST00000216392
5a
ENSE00000657192
chr14:
51390818-51390687
132
PYGL_HUMAN
177-220
44
2
A:176-219
B:176-219
44
44
1.6
ENST00000216392
6
ENSE00000657191
chr14:
51387785-51387674
112
PYGL_HUMAN
221-258
38
2
A:220-249
B:220-249
30
30
1.7
ENST00000216392
7
ENSE00001647495
chr14:
51387341-51387259
83
PYGL_HUMAN
258-285
28
2
A:260-284
B:260-284
25
25
1.8a
ENST00000216392
8a
ENSE00001507082
chr14:
51383823-51383680
144
PYGL_HUMAN
286-333
48
2
A:285-332 (gaps)
B:285-332 (gaps)
48
48
1.9
ENST00000216392
9
ENSE00001800310
chr14:
51383452-51383360
93
PYGL_HUMAN
334-364
31
2
A:333-363
B:333-363
31
31
1.10a
ENST00000216392
10a
ENSE00000657186
chr14:
51382689-51382543
147
PYGL_HUMAN
365-413
49
2
A:364-412
B:364-412
49
49
1.11
ENST00000216392
11
ENSE00000657184
chr14:
51382217-51382054
164
PYGL_HUMAN
414-468
55
2
A:413-467
B:413-467
55
55
1.12
ENST00000216392
12
ENSE00000657182
chr14:
51381533-51381419
115
PYGL_HUMAN
468-506
39
2
A:467-505
B:467-505
39
39
1.13
ENST00000216392
13
ENSE00000657181
chr14:
51379848-51379747
102
PYGL_HUMAN
507-540
34
2
A:506-539
B:506-539
34
34
1.14a
ENST00000216392
14a
ENSE00000657180
chr14:
51379021-51378874
148
PYGL_HUMAN
541-590
50
2
A:540-589
B:540-589
50
50
1.15a
ENST00000216392
15a
ENSE00000657178
chr14:
51378754-51378696
59
PYGL_HUMAN
590-609
20
2
A:589-608
B:589-608
20
20
1.16b
ENST00000216392
16b
ENSE00000657176
chr14:
51378589-51378448
142
PYGL_HUMAN
610-657
48
2
A:609-656
B:609-656
48
48
1.17b
ENST00000216392
17b
ENSE00001681548
chr14:
51376820-51376613
208
PYGL_HUMAN
657-726
70
2
A:656-725
B:656-725
70
70
1.18
ENST00000216392
18
ENSE00000657174
chr14:
51375673-51375539
135
PYGL_HUMAN
726-771
46
2
A:725-770
B:725-770
46
46
1.19a
ENST00000216392
19a
ENSE00000657173
chr14:
51375055-51374989
67
PYGL_HUMAN
771-793
23
2
A:770-792
B:770-792
23
23
1.20a
ENST00000216392
20a
ENSE00002201324
chr14:
51372274-51371939
336
PYGL_HUMAN
794-847
54
2
A:793-830
B:793-830
38
38
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1exva_ (A:)
1b: SCOP_d1exvb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
UDP-Glycosyltransferase/glycogen phosphorylase
(296)
Superfamily
:
UDP-Glycosyltransferase/glycogen phosphorylase
(296)
Family
:
Oligosaccharide phosphorylase
(199)
Protein domain
:
Glycogen phosphorylase
(86)
Human (Homo sapiens) [TaxId: 9606]
(16)
1a
d1exva_
A:
1b
d1exvb_
B:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1exvA02 (A:486-812)
1b: CATH_1exvB02 (B:486-812)
1c: CATH_1exvA01 (A:23-485,A:813-828)
1d: CATH_1exvB01 (B:23-485,B:813-828)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Glycogen Phosphorylase B;
(202)
Human (Homo sapiens)
(16)
1a
1exvA02
A:486-812
1b
1exvB02
B:486-812
1c
1exvA01
A:23-485,A:813-828
1d
1exvB01
B:23-485,B:813-828
[
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
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 (273 KB)
Header - Asym.Unit
Biol.Unit 1 (267 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
1EXV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help