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1Z8D
Asym. Unit
Info
Asym.Unit (149 KB)
Biol.Unit 1 (284 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MUSCLE GLYCOGEN PHOSPHORYLASE A WITH AMP AND GLUCOSE
Authors
:
C. M. Lukacs, N. G. Oikonomakos, R. L. Crowther, L. N. Hong, R. U. Kammlot W. Levin, S. Li, C. M. Liu, D. Lucas-Mcgady, S. Pietranico, L. Reik
Date
:
30 Mar 05 (Deposition) - 21 Mar 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. M. Lukacs, N. G. Oikonomakos, R. L. Crowther, L. N. Hong, R. U. Kammlott, W. Levin, S. Li, C. M. Liu, D. Lucas-Mcgady, S. Pietranico, L. Reik
The Crystal Structure Of Human Muscle Glycogen Phosphorylas A With Bound Glucose And Amp: An Intermediate Conformation With T-State And R-State Features.
Proteins V. 63 1123 2006
[
close entry info
]
Hetero Components
(5, 5)
Info
All Hetero Components
1a: ADENINE (ADEa)
2a: ADENOSINE MONOPHOSPHATE (AMPa)
3a: ALPHA-D-GLUCOSE (GLCa)
4a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
5a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADE
1
Ligand/Ion
ADENINE
2
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
3
GLC
1
Ligand/Ion
ALPHA-D-GLUCOSE
4
LLP
1
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
5
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:136 , LEU A:139 , 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:1043 , HOH A:1053 , HOH A:1093
BINDING SITE FOR RESIDUE GLC A 901
2
AC2
SOFTWARE
ASP A:42 , ASN A:44 , TRP A:67 , GLN A:71 , TYR A:75 , ARG A:309 , ARG A:310 , LYS A:315 , PHE A:316 , GLY A:317 , CYS A:318 , HOH A:950 , HOH A:951 , HOH A:953
BINDING SITE FOR RESIDUE AMP A 900
3
AC3
SOFTWARE
PHE A:285 , ALA A:610 , GLY A:612 , TYR A:613
BINDING SITE FOR RESIDUE ADE A 902
[
close Site info
]
SAPs(SNPs)/Variants
(18, 18)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_014002 (L115P, chain A, )
02: VAR_014003 (R193W, chain A, )
03: VAR_003431 (G204S, chain A, )
04: VAR_014004 (L291P, chain A, )
05: VAR_014005 (E348K, chain A, )
06: VAR_003432 (L396P, chain A, )
07: VAR_061198 (R413G, chain A, )
08: VAR_014006 (T487N, chain A, )
09: VAR_003433 (K542T, chain A, )
10: VAR_014007 (R601W, chain A, )
11: VAR_003434 (E654K, chain A, )
12: VAR_014008 (A659D, chain A, )
13: VAR_014009 (Q665E, chain A, )
14: VAR_014010 (N684Y, chain A, )
15: VAR_014011 (G685R, chain A, )
16: VAR_014012 (A686P, chain A, )
17: VAR_014013 (A703V, chain A, )
18: VAR_014015 (W797R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_014002
L
116
P
PYGM_HUMAN
Disease (GSD5)
---
A
L
115
P
02
UniProt
VAR_014003
R
194
W
PYGM_HUMAN
Disease (GSD5)
---
A
R
193
W
03
UniProt
VAR_003431
G
205
S
PYGM_HUMAN
Disease (GSD5)
119103251
A
G
204
S
04
UniProt
VAR_014004
L
292
P
PYGM_HUMAN
Disease (GSD5)
---
A
L
291
P
05
UniProt
VAR_014005
E
349
K
PYGM_HUMAN
Disease (GSD5)
---
A
E
348
K
06
UniProt
VAR_003432
L
397
P
PYGM_HUMAN
Disease (GSD5)
---
A
L
396
P
07
UniProt
VAR_061198
R
414
G
PYGM_HUMAN
Polymorphism
11231866
A
R
413
G
08
UniProt
VAR_014006
T
488
N
PYGM_HUMAN
Disease (GSD5)
---
A
T
487
N
09
UniProt
VAR_003433
K
543
T
PYGM_HUMAN
Disease (GSD5)
---
A
K
542
T
10
UniProt
VAR_014007
R
602
W
PYGM_HUMAN
Disease (GSD5)
---
A
R
601
W
11
UniProt
VAR_003434
E
655
K
PYGM_HUMAN
Disease (GSD5)
---
A
E
654
K
12
UniProt
VAR_014008
A
660
D
PYGM_HUMAN
Disease (GSD5)
---
A
A
659
D
13
UniProt
VAR_014009
Q
666
E
PYGM_HUMAN
Disease (GSD5)
---
A
Q
665
E
14
UniProt
VAR_014010
N
685
Y
PYGM_HUMAN
Disease (GSD5)
---
A
N
684
Y
15
UniProt
VAR_014011
G
686
R
PYGM_HUMAN
Disease (GSD5)
---
A
G
685
R
16
UniProt
VAR_014012
A
687
P
PYGM_HUMAN
Disease (GSD5)
---
A
A
686
P
17
UniProt
VAR_014013
A
704
V
PYGM_HUMAN
Disease (GSD5)
---
A
A
703
V
18
UniProt
VAR_014015
W
798
R
PYGM_HUMAN
Disease (GSD5)
---
A
W
797
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PHOSPHORYLASE (A: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.
PYGM_HUMAN
673-685
1
A:672-684
[
close PROSITE info
]
Exons
(20, 20)
Info
All Exons
Exon 1.1a (A:2-80 (gaps))
Exon 1.2 (A:81-114)
Exon 1.3 (A:115-141)
Exon 1.4a (A:141-175)
Exon 1.5 (A:176-219)
Exon 1.6 (A:220-249)
Exon 1.7b (A:261-284)
Exon 1.8 (A:285-332)
Exon 1.9b (A:333-363)
Exon 1.10 (A:364-412)
Exon 1.11b (A:413-467)
Exon 1.12 (A:467-505)
Exon 1.13 (A:506-539)
Exon 1.14a (A:540-589)
Exon 1.15 (A:589-608)
Exon 1.16a (A:609-656)
Exon 1.17 (A:656-725)
Exon 1.18b (A:725-770)
Exon 1.19 (A:770-792)
Exon 1.20b (A:793-836)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4a
05: Boundary 1.4a/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7b
08: Boundary 1.7b/1.8
09: Boundary 1.8/1.9b
10: Boundary 1.9b/1.10
11: Boundary 1.10/1.11b
12: Boundary 1.11b/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14a
15: Boundary 1.14a/1.15
16: Boundary 1.15/1.16a
17: Boundary 1.16a/1.17
18: Boundary 1.17/1.18b
19: Boundary 1.18b/1.19
20: Boundary 1.19/1.20b
21: Boundary 1.20b/-
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
ENST00000164139
1a
ENSE00001120049
chr11:
64527769-64527128
642
PYGM_HUMAN
1-81
81
1
A:2-80 (gaps)
79
1.2
ENST00000164139
2
ENSE00001171792
chr11:
64526176-64526075
102
PYGM_HUMAN
82-115
34
1
A:81-114
34
1.3
ENST00000164139
3
ENSE00001171784
chr11:
64525987-64525909
79
PYGM_HUMAN
116-142
27
1
A:115-141
27
1.4a
ENST00000164139
4a
ENSE00001171774
chr11:
64525821-64525718
104
PYGM_HUMAN
142-176
35
1
A:141-175
35
1.5
ENST00000164139
5
ENSE00000863658
chr11:
64525382-64525251
132
PYGM_HUMAN
177-220
44
1
A:176-219
44
1.6
ENST00000164139
6
ENSE00001621025
chr11:
64523030-64522919
112
PYGM_HUMAN
221-258
38
1
A:220-249
30
1.7b
ENST00000164139
7b
ENSE00001767104
chr11:
64522827-64522745
83
PYGM_HUMAN
258-285
28
1
A:261-284
24
1.8
ENST00000164139
8
ENSE00000863655
chr11:
64522308-64522165
144
PYGM_HUMAN
286-333
48
1
A:285-332
48
1.9b
ENST00000164139
9b
ENSE00000730810
chr11:
64521817-64521725
93
PYGM_HUMAN
334-364
31
1
A:333-363
31
1.10
ENST00000164139
10
ENSE00000863653
chr11:
64521497-64521351
147
PYGM_HUMAN
365-413
49
1
A:364-412
49
1.11b
ENST00000164139
11b
ENSE00000730806
chr11:
64521154-64520991
164
PYGM_HUMAN
414-468
55
1
A:413-467
55
1.12
ENST00000164139
12
ENSE00000863651
chr11:
64520659-64520545
115
PYGM_HUMAN
468-506
39
1
A:467-505
39
1.13
ENST00000164139
13
ENSE00000863650
chr11:
64519976-64519875
102
PYGM_HUMAN
507-540
34
1
A:506-539
34
1.14a
ENST00000164139
14a
ENSE00001722365
chr11:
64519543-64519396
148
PYGM_HUMAN
541-590
50
1
A:540-589
50
1.15
ENST00000164139
15
ENSE00000730796
chr11:
64519127-64519069
59
PYGM_HUMAN
590-609
20
1
A:589-608
20
1.16a
ENST00000164139
16a
ENSE00000730794
chr11:
64518938-64518797
142
PYGM_HUMAN
610-657
48
1
A:609-656
48
1.17
ENST00000164139
17
ENSE00000730792
chr11:
64518055-64517848
208
PYGM_HUMAN
657-726
70
1
A:656-725
70
1.18b
ENST00000164139
18b
ENSE00000730789
chr11:
64514830-64514696
135
PYGM_HUMAN
726-771
46
1
A:725-770
46
1.19
ENST00000164139
19
ENSE00001171666
chr11:
64514459-64514393
67
PYGM_HUMAN
771-793
23
1
A:770-792
23
1.20b
ENST00000164139
20b
ENSE00001954096
chr11:
64514280-64513861
420
PYGM_HUMAN
794-842
49
1
A:793-836
44
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1z8da_ (A:)
View:
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Classes
(
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(
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Folds
(
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(
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Superfamilies
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(
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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
:
automated matches
(106)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1z8da_
A:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1z8dA02 (A:486-812)
1b: CATH_1z8dA01 (A:10-485,A:813-832)
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Homologous Superfamilies
(
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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)
Human (Homo sapiens)
(16)
1a
1z8dA02
A:486-812
1b
1z8dA01
A:10-485,A:813-832
[
close CATH info
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Phosphorylase_1z8dA01 (A:111-829)
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Clans
(
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Families
(
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(
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Organisms
(
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(
)
Clan
:
GT-B
(132)
Family
:
Phosphorylase
(83)
Homo sapiens (Human)
(8)
1a
Phosphorylase-1z8dA01
A:111-829
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