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3QVB
Biol. Unit 1
Info
Asym.Unit (92 KB)
Biol.Unit 1 (171 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH MANGANESE AND UDP
Authors
:
A. Chaikuad, D. S. Froese, W. W. Yue, E. Krysztofinska, F. Von Delft, J. C. H. Arrowsmith, A. M. Edwards, C. Bountra, U. Oppermann, Structural Consortium (Sgc)
Date
:
25 Feb 11 (Deposition) - 23 Mar 11 (Release) - 11 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.26
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Structural Genomics, Structural Genomics Consortium, (Sgc), Transferase, Glycosyltransferase, Glycogen Biosynthesis, Glycosylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Chaikuad, D. S. Froese, G. Berridge, F. Von Delft, U. Oppermann, W. W. Yue
Conformational Plasticity Of Glycogenin And Its Maltosaccharide Substrate During Glycogen Biogenesis.
Proc. Natl. Acad. Sci. Usa V. 108 21028 2011
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
2a: MANGANESE (II) ION (MNa)
3a: URIDINE-5'-DIPHOSPHATE (UDPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
3
UDP
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:102 , ASP A:104 , HIS A:212 , UDP A:264
BINDING SITE FOR RESIDUE MN A 263
2
AC2
SOFTWARE
LEU A:9 , THR A:10 , THR A:11 , TYR A:15 , VAL A:82 , ASP A:102 , ALA A:103 , ASP A:104 , HIS A:212 , LEU A:214 , GLY A:215 , LYS A:218 , MN A:263 , HOH A:388
BINDING SITE FOR RESIDUE UDP A 264
3
AC3
SOFTWARE
HIS A:29 , ARG A:30 , ASN A:110
BINDING SITE FOR RESIDUE EDO A 265
4
AC4
SOFTWARE
THR A:93 , SER A:142 , VAL A:143 , GLU A:144
BINDING SITE FOR RESIDUE EDO A 266
5
AC5
SOFTWARE
GLU A:119 , LEU A:120 , SER A:173 , LYS A:181 , HOH A:364
BINDING SITE FOR RESIDUE EDO A 267
6
AC6
SOFTWARE
HIS A:88 , LEU A:92 , HOH A:308
BINDING SITE FOR RESIDUE EDO A 268
7
AC7
SOFTWARE
SER A:44 , ASP A:45 , SER A:46 , SER A:158 , PHE A:159 , ASP A:160 , GLY A:161
BINDING SITE FOR RESIDUE EDO A 269
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SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_072706 (A16P, chain A, )
2: VAR_063768 (T83M, chain A, )
3: VAR_072707 (D102H, chain A, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_072706
A
16
P
GLYG_HUMAN
Disease (PGBM2)
---
A
A
16
P
2
UniProt
VAR_063768
T
83
M
GLYG_HUMAN
Disease (GSD15)
---
A
T
83
M
3
UniProt
VAR_072707
D
102
H
GLYG_HUMAN
Disease (PGBM2)
---
A
D
102
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3qvba_ (A:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
Glycogenin
(27)
Protein domain
:
Glycogenin
(27)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d3qvba_
A:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Glyco_transf_8_3qvbA01 (A:6-224)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
GT-A
(172)
Family
:
Glyco_transf_8
(13)
Homo sapiens (Human)
(4)
1a
Glyco_transf_8-3qvbA01
A:6-224
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Chain A
Asymmetric Unit 1
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Asym.Unit (92 KB)
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