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3DD1
Asym. Unit
Info
Asym.Unit (285 KB)
Biol.Unit 1 (278 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCOGEN PHOPHORYLASE COMPLEXED WITH AN ANTHRANILIMIDE BASED INHIBITOR GSK254
Authors
:
R. T. Nolte
Date
:
04 Jun 08 (Deposition) - 21 Apr 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.57
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycogen Phosphorylase Hlgp, Diabetes, Allosteric Enzyme, Carbohydrate Metabolism, Disease Mutation, Glycogen Metabolism, Glycogen Storage Disease, Glycosyltransferase, Nucleotide-Binding, Phosphoprotein, Pyridoxal Phosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. A. Thomson, P. Banker, D. M. Bickett, J. A. Boucheron, H. L. Carter, D. C. Clancy, J. P. Cooper, S. H. Dickerson, D. M. Garrido, R. T. Nolte, A. J. Peat, L. R. Sheckler, S. M. Sparks, F. X. Tavares, L. Wang, T. Y. Wang, J. E. Weiel
Anthranilimide Based Glycogen Phosphorylase Inhibitors For The Treatment Of Type 2 Diabetes. Part 3: X-Ray Crystallographic Characterization, Core And Urea Optimization And In Vivo Efficacy.
Bioorg. Med. Chem. Lett. V. 19 1177 2009
[
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Hetero Components
(7, 16)
Info
All Hetero Components
1a: 2-CYCLOHEXYL-N-[(3-{[(2,4,6-TRIMET... (25Da)
1b: 2-CYCLOHEXYL-N-[(3-{[(2,4,6-TRIMET... (25Db)
2a: CAFFEINE (CFFa)
2b: CAFFEINE (CFFb)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
4c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
4d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
4e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
5a: 1-N-ACETYL-BETA-D-GLUCOSAMINE (NBGa)
5b: 1-N-ACETYL-BETA-D-GLUCOSAMINE (NBGb)
6a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
6b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
7a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
25D
2
Ligand/Ion
2-CYCLOHEXYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-D-ALANINE
2
CFF
2
Ligand/Ion
CAFFEINE
3
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
MPD
5
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
NBG
2
Ligand/Ion
1-N-ACETYL-BETA-D-GLUCOSAMINE
6
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
7
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(14, 14)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:135 , LEU A:136 , ASN A:284 , ASP A:339 , 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:973 , HOH A:1061 , HOH A:1135 , HOH A:1150
BINDING SITE FOR RESIDUE NBG A 901
02
AC2
SOFTWARE
LEU B:136 , 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:1109 , HOH B:1126
BINDING SITE FOR RESIDUE NBG B 901
03
AC3
SOFTWARE
TYR A:90 , TRP A:491 , LYS A:568 , LYS A:574 , TYR A:648 , ARG A:649 , VAL A:650 , GLY A:675 , THR A:676 , GLY A:677 , LYS A:680 , HOH A:1002 , HOH A:1059 , HOH A:1061 , HOH A:1088 , HOH A:1156
BINDING SITE FOR RESIDUE PLP A 902
04
AC4
SOFTWARE
ASN A:282 , PHE A:285 , HIS A:571 , ALA A:610 , GLY A:612 , TYR A:613 , HOH A:1066
BINDING SITE FOR RESIDUE CFF A 903
05
AC5
SOFTWARE
TRP A:67 , ILE A:68 , GLN A:71 , GLN A:72 , TYR A:75 , TYR A:155 , ARG A:193 , ASP A:227 , THR A:240 , ARG A:310 , ALA A:313 , HOH A:976 , HOH A:1173 , VAL B:40 , LYS B:41 , ASP B:42 , VAL B:45
BINDING SITE FOR RESIDUE 25D A 905
06
AC6
SOFTWARE
TYR B:90 , 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:919 , HOH B:961 , HOH B:976 , HOH B:1067 , HOH B:1123
BINDING SITE FOR RESIDUE PLP B 902
07
AC7
SOFTWARE
ASN B:282 , PHE B:285 , HIS B:571 , ALA B:610 , GLY B:612 , TYR B:613 , HOH B:1082 , HOH B:1115
BINDING SITE FOR RESIDUE CFF B 903
08
AC8
SOFTWARE
ILE B:170 , ARG B:171 , ASP B:172 , GLY B:173 , GLU B:552 , GLU B:646
BINDING SITE FOR RESIDUE MES B 904
09
AC9
SOFTWARE
ARG B:49 , ARG B:93 , GLU B:124 , ILE B:125 , GLU B:127 , HOH B:1004
BINDING SITE FOR RESIDUE MES B 905
10
BC1
SOFTWARE
VAL A:40 , ASP A:42 , VAL A:45 , TRP B:67 , GLN B:71 , GLN B:72 , ARG B:193 , PHE B:196 , ASP B:227 , THR B:240 , ARG B:242 , ARG B:310
BINDING SITE FOR RESIDUE 25D B 906
11
BC2
SOFTWARE
HIS A:201 , TRP A:215 , ARG A:351 , HOH A:914 , HOH A:1080 , GLY B:508
BINDING SITE FOR RESIDUE MPD A 906
12
BC3
SOFTWARE
ALA A:322 , ILE A:356 , GLU A:357 , LYS A:358 , GLU B:501 , GLU B:509
BINDING SITE FOR RESIDUE MPD A 907
13
BC4
SOFTWARE
ASP A:746 , PHE A:766 , PRO B:752
BINDING SITE FOR RESIDUE MPD A 908
14
BC5
SOFTWARE
ASP B:769 , HOH B:1079
BINDING SITE FOR RESIDUE MPD B 907
[
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:12-80 | 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:220-251 | B:220-257)
Exon 1.7 (A:260-284 | B:257-284)
Exon 1.8a (A:285-332 | 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:12-80
B:23-80
69
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:220-251
B:220-257
32
38
1.7
ENST00000216392
7
ENSE00001647495
chr14:
51387341-51387259
83
PYGL_HUMAN
258-285
28
2
A:260-284
B:257-284
25
28
1.8a
ENST00000216392
8a
ENSE00001507082
chr14:
51383823-51383680
144
PYGL_HUMAN
286-333
48
2
A:285-332
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
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3dd1a_ (A:)
1b: SCOP_d3dd1b_ (B:)
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Protein Domains
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(
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Organisms
(
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(
)
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
d3dd1a_
A:
1b
d3dd1b_
B:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3dd1A02 (A:486-812)
1b: CATH_3dd1A01 (A:12-485,A:813-830)
1c: CATH_3dd1B02 (B:486-812)
1d: CATH_3dd1B01 (B:23-485,B:813-828)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Glycogen Phosphorylase B;
(202)
Homo sapiens. Organism_taxid: 9606.
(3)
1a
3dd1A02
A:486-812
1b
3dd1A01
A:12-485,A:813-830
1c
3dd1B02
B:486-812
1d
3dd1B01
B:23-485,B:813-828
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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