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Asym. Unit
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Asym.Unit (272 KB)
Biol.Unit 1 (267 KB)
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(1)
Title
:
HUMAN LIVER GLYCOGEN PHOSPHORYLASE COMPLEXED WITH N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE
Authors
:
V. L. Rath, M. Ammirati, P. K. Lemotte, K. F. Fennell, M. M. Mansour, D. E. T. R. Hynes, G. K. Schulte, D. J. Wasilko, J. Pandit
Date
:
17 Jul 00 (Deposition) - 25 Aug 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
:
Phosphorylated Protein, Allosteric, Glucose Analog, Inhibitor, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. L. Rath, M. Ammirati, P. K. Lemotte, K. F. Fennell, M. N. Mansour, D. E. Danley, T. R. Hynes, G. K. Schulte, D. J. Wasilko, J. Pandit
Activation Of Human Liver Glycogen Phosphorylase By Alteration Of The Secondary Structure And Packing Of The Catalytic Core.
Mol. Cell V. 6 139 2000
[
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 1-N-ACETYL-BETA-D-GLUCOSAMINE (NBGa)
1b: 1-N-ACETYL-BETA-D-GLUCOSAMINE (NBGb)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NBG
2
Ligand/Ion
1-N-ACETYL-BETA-D-GLUCOSAMINE
2
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:136 , ASN A:284 , HIS A:377 , THR A:378 , VAL A:455 , ASN A:484 , TYR A:573 , GLU A:672 , ALA A:673 , SER A:674 , GLY A:675 , HOH A:2052 , HOH A:2173 , HOH A:2225
BINDING SITE FOR RESIDUE NBG A 861
2
AC2
SOFTWARE
GLY B:1135 , LEU B:1136 , LEU B:1139 , ASN B:1284 , ASP B:1339 , HIS B:1377 , VAL B:1455 , ASN B:1484 , TYR B:1573 , GLU B:1672 , ALA B:1673 , SER B:1674 , GLY B:1675 , HOH B:2142 , HOH B:2153 , HOH B:2207 , HOH B:2253
BINDING SITE FOR RESIDUE NBG B 1861
3
AC3
SOFTWARE
TYR A:90 , 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:2014 , HOH A:2055 , HOH A:2162
BINDING SITE FOR RESIDUE PLP A 860
4
AC4
SOFTWARE
GLY B:1134 , TRP B:1491 , LYS B:1568 , LYS B:1574 , ARG B:1649 , VAL B:1650 , ALA B:1653 , GLY B:1675 , THR B:1676 , GLY B:1677 , LYS B:1680 , HOH B:2049 , HOH B:2056 , HOH B:2239
BINDING SITE FOR RESIDUE PLP B 1860
[
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SAPs(SNPs)/Variants
(8, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_007907 (V1221I, chain A/B, )
2: VAR_013095 (V1230E, chain A/B, )
3: VAR_007908 (N1338S, chain A/B, )
4: VAR_007909 (N1376K, chain A/B, )
5: VAR_034425 (R1424P, chain A/B, )
6: VAR_034426 (V1697G, chain A/B, )
7: VAR_013096 (R1714S, chain A/B, )
8: VAR_034427 (I1805L, 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
1221
I
2
UniProt
VAR_013095
V
231
E
PYGL_HUMAN
Polymorphism
1042195
A
B
V
230
1230
E
3
UniProt
VAR_007908
N
339
S
PYGL_HUMAN
Disease (GSD6)
---
A
B
N
338
1338
S
4
UniProt
VAR_007909
N
377
K
PYGL_HUMAN
Disease (GSD6)
---
A
B
N
376
1376
K
5
UniProt
VAR_034425
R
425
P
PYGL_HUMAN
Polymorphism
2228499
A
B
R
424
1424
P
6
UniProt
VAR_034426
V
698
G
PYGL_HUMAN
Polymorphism
35831273
A
B
V
697
1697
G
7
UniProt
VAR_013096
R
715
S
PYGL_HUMAN
Polymorphism
1042210
A
B
R
714
1714
S
8
UniProt
VAR_034427
I
806
L
PYGL_HUMAN
Polymorphism
34313873
A
B
I
805
1805
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:1672-1684)
;
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:1672-1684
[
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]
Exons
(20, 40)
Info
All Exons
Exon 1.1a (A:23-80 | B:1023-1080)
Exon 1.2 (A:81-114 | B:1081-1114)
Exon 1.3b (A:115-141 | B:1115-1141)
Exon 1.4a (A:141-175 | B:1141-1175)
Exon 1.5a (A:176-219 | B:1176-1219)
Exon 1.6 (A:220-249 | B:1220-1249)
Exon 1.7 (A:260-284 | B:1260-1284)
Exon 1.8a (A:285-332 (gaps) | B:1285-1332 (ga...)
Exon 1.9 (A:333-363 | B:1333-1363)
Exon 1.10a (A:364-412 | B:1364-1412)
Exon 1.11 (A:413-467 | B:1413-1467)
Exon 1.12 (A:467-505 | B:1467-1505)
Exon 1.13 (A:506-539 | B:1506-1539)
Exon 1.14a (A:540-589 | B:1540-1589)
Exon 1.15a (A:589-608 | B:1589-1608)
Exon 1.16b (A:609-656 | B:1609-1656)
Exon 1.17b (A:656-725 | B:1656-1725)
Exon 1.18 (A:725-770 | B:1725-1770)
Exon 1.19a (A:770-792 | B:1770-1792)
Exon 1.20a (A:793-831 | B:1793-1831)
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:1023-1080
58
58
1.2
ENST00000216392
2
ENSE00000657195
chr14:
51404555-51404454
102
PYGL_HUMAN
82-115
34
2
A:81-114
B:1081-1114
34
34
1.3b
ENST00000216392
3b
ENSE00000657194
chr14:
51401903-51401825
79
PYGL_HUMAN
116-142
27
2
A:115-141
B:1115-1141
27
27
1.4a
ENST00000216392
4a
ENSE00000657193
chr14:
51398494-51398391
104
PYGL_HUMAN
142-176
35
2
A:141-175
B:1141-1175
35
35
1.5a
ENST00000216392
5a
ENSE00000657192
chr14:
51390818-51390687
132
PYGL_HUMAN
177-220
44
2
A:176-219
B:1176-1219
44
44
1.6
ENST00000216392
6
ENSE00000657191
chr14:
51387785-51387674
112
PYGL_HUMAN
221-258
38
2
A:220-249
B:1220-1249
30
30
1.7
ENST00000216392
7
ENSE00001647495
chr14:
51387341-51387259
83
PYGL_HUMAN
258-285
28
2
A:260-284
B:1260-1284
25
25
1.8a
ENST00000216392
8a
ENSE00001507082
chr14:
51383823-51383680
144
PYGL_HUMAN
286-333
48
2
A:285-332 (gaps)
B:1285-1332 (gaps)
48
48
1.9
ENST00000216392
9
ENSE00001800310
chr14:
51383452-51383360
93
PYGL_HUMAN
334-364
31
2
A:333-363
B:1333-1363
31
31
1.10a
ENST00000216392
10a
ENSE00000657186
chr14:
51382689-51382543
147
PYGL_HUMAN
365-413
49
2
A:364-412
B:1364-1412
49
49
1.11
ENST00000216392
11
ENSE00000657184
chr14:
51382217-51382054
164
PYGL_HUMAN
414-468
55
2
A:413-467
B:1413-1467
55
55
1.12
ENST00000216392
12
ENSE00000657182
chr14:
51381533-51381419
115
PYGL_HUMAN
468-506
39
2
A:467-505
B:1467-1505
39
39
1.13
ENST00000216392
13
ENSE00000657181
chr14:
51379848-51379747
102
PYGL_HUMAN
507-540
34
2
A:506-539
B:1506-1539
34
34
1.14a
ENST00000216392
14a
ENSE00000657180
chr14:
51379021-51378874
148
PYGL_HUMAN
541-590
50
2
A:540-589
B:1540-1589
50
50
1.15a
ENST00000216392
15a
ENSE00000657178
chr14:
51378754-51378696
59
PYGL_HUMAN
590-609
20
2
A:589-608
B:1589-1608
20
20
1.16b
ENST00000216392
16b
ENSE00000657176
chr14:
51378589-51378448
142
PYGL_HUMAN
610-657
48
2
A:609-656
B:1609-1656
48
48
1.17b
ENST00000216392
17b
ENSE00001681548
chr14:
51376820-51376613
208
PYGL_HUMAN
657-726
70
2
A:656-725
B:1656-1725
70
70
1.18
ENST00000216392
18
ENSE00000657174
chr14:
51375673-51375539
135
PYGL_HUMAN
726-771
46
2
A:725-770
B:1725-1770
46
46
1.19a
ENST00000216392
19a
ENSE00000657173
chr14:
51375055-51374989
67
PYGL_HUMAN
771-793
23
2
A:770-792
B:1770-1792
23
23
1.20a
ENST00000216392
20a
ENSE00002201324
chr14:
51372274-51371939
336
PYGL_HUMAN
794-847
54
2
A:793-831
B:1793-1831
39
39
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1fc0a_ (A:)
1b: SCOP_d1fc0b_ (B:)
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(
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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
d1fc0a_
A:
1b
d1fc0b_
B:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1fc0A02 (A:486-812)
1b: CATH_1fc0B02 (B:1486-1812)
1c: CATH_1fc0A01 (A:23-485,A:813-829)
1d: CATH_1fc0B01 (B:1023-1485,B:1813-1829)
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(
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Organisms
(
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(
)
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
1fc0A02
A:486-812
1b
1fc0B02
B:1486-1812
1c
1fc0A01
A:23-485,A:813-829
1d
1fc0B01
B:1023-1485,B:1813-1829
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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