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3T7O
Asym. Unit
Info
Asym.Unit (194 KB)
Biol.Unit 1 (187 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH MANGANESE, UDP-GLUCOSE AND GLUCOSE
Authors
:
A. Chaikuad, D. S. Froese, E. Krysztofinska, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, C. Bountra, U. Oppermann, W. W. Yue, St Genomics Consortium (Sgc)
Date
:
30 Jul 11 (Deposition) - 31 Aug 11 (Release) - 11 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
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
(4, 24)
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)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
2a: ALPHA-D-GLUCOSE (GLCa)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
4a: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGa)
4b: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
19
Ligand/Ion
1,2-ETHANEDIOL
2
GLC
1
Ligand/Ion
ALPHA-D-GLUCOSE
3
MN
2
Ligand/Ion
MANGANESE (II) ION
4
UPG
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE-GLUCOSE
[
close Hetero Component info
]
Sites
(24, 24)
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)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:77 , ASP A:125 , PRO A:126 , GLN A:164 , UPG A:265 , HOH A:414 , HOH A:482 , HOH A:500 , SER B:196
BINDING SITE FOR RESIDUE GLC A 263
02
AC2
SOFTWARE
ASP A:102 , ASP A:104 , HIS A:212 , UPG A:265
BINDING SITE FOR RESIDUE MN A 264
03
AC3
SOFTWARE
LEU A:9 , THR A:10 , THR A:11 , ASN A:12 , TYR A:15 , ARG A:77 , LEU A:80 , THR A:83 , LYS A:86 , ASP A:102 , ALA A:103 , ASP A:104 , ASN A:133 , SER A:134 , GLY A:135 , ASP A:160 , GLY A:162 , ASP A:163 , GLN A:164 , HIS A:212 , LEU A:214 , GLY A:215 , LYS A:218 , GLC A:263 , MN A:264
BINDING SITE FOR RESIDUE UPG A 265
04
AC4
SOFTWARE
SER A:142 , VAL A:143 , GLU A:144
BINDING SITE FOR RESIDUE EDO A 266
05
AC5
SOFTWARE
ASP A:178 , ILE A:179 , ILE B:179
BINDING SITE FOR RESIDUE EDO A 267
06
AC6
SOFTWARE
ARG A:34 , ARG B:48
BINDING SITE FOR RESIDUE EDO A 268
07
AC7
SOFTWARE
GLU A:119 , LEU A:120 , SER A:173 , TRP A:174 , LYS A:181 , HOH A:280 , HOH A:305
BINDING SITE FOR RESIDUE EDO A 269
08
AC8
SOFTWARE
HIS A:29 , ASN A:110 , HOH A:300
BINDING SITE FOR RESIDUE EDO A 270
09
AC9
SOFTWARE
ARG A:33
BINDING SITE FOR RESIDUE EDO A 271
10
BC1
SOFTWARE
LYS A:97 , PHE A:115
BINDING SITE FOR RESIDUE EDO A 272
11
BC2
SOFTWARE
PHE A:171 , SER A:172 , SER A:173 , HOH A:370
BINDING SITE FOR RESIDUE EDO A 273
12
BC3
SOFTWARE
GLN A:28 , HIS A:29 , LEU A:108 , HOH A:333 , HOH A:510
BINDING SITE FOR RESIDUE EDO A 274
13
BC4
SOFTWARE
PRO A:41 , ARG A:48 , HOH A:471
BINDING SITE FOR RESIDUE EDO A 275
14
BC5
SOFTWARE
ASP B:102 , ASP B:104 , HIS B:212 , UPG B:264
BINDING SITE FOR RESIDUE MN B 263
15
BC6
SOFTWARE
LEU B:9 , THR B:10 , THR B:11 , ASN B:12 , TYR B:15 , ARG B:77 , LEU B:80 , THR B:83 , LYS B:86 , ASP B:102 , ALA B:103 , ASP B:104 , ASN B:133 , SER B:134 , GLY B:135 , ASP B:160 , GLY B:162 , ASP B:163 , GLN B:164 , HIS B:212 , GLY B:215 , LYS B:218 , MN B:263 , HOH B:319
BINDING SITE FOR RESIDUE UPG B 264
16
BC7
SOFTWARE
HIS B:29 , ARG B:30 , ASN B:110 , HOH B:325 , HOH B:466
BINDING SITE FOR RESIDUE EDO B 265
17
BC8
SOFTWARE
GLU B:119 , LEU B:120 , SER B:173 , TRP B:174 , LYS B:181 , HOH B:331
BINDING SITE FOR RESIDUE EDO B 266
18
BC9
SOFTWARE
SER B:91 , GLN B:94 , HOH B:464 , HOH B:467
BINDING SITE FOR RESIDUE EDO B 267
19
CC1
SOFTWARE
ARG B:34 , GLU B:57 , EDO B:269 , EDO B:273 , HOH B:465 , HOH B:555 , HOH B:577
BINDING SITE FOR RESIDUE EDO B 268
20
CC2
SOFTWARE
ARG B:34 , EDO B:268
BINDING SITE FOR RESIDUE EDO B 269
21
CC3
SOFTWARE
THR B:93 , GLN B:94 , SER B:96 , HOH B:553
BINDING SITE FOR RESIDUE EDO B 270
22
CC4
SOFTWARE
VAL B:58 , HOH B:429
BINDING SITE FOR RESIDUE EDO B 271
23
CC5
SOFTWARE
HOH B:453
BINDING SITE FOR RESIDUE EDO B 272
24
CC6
SOFTWARE
GLU B:57 , GLN B:94 , EDO B:268 , HOH B:279 , HOH B:453 , HOH B:465 , HOH B:576
BINDING SITE FOR RESIDUE EDO B 273
[
close Site info
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SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_072706 (A16P, chain A/B, )
2: VAR_063768 (T83M, chain A/B, )
3: VAR_072707 (D102H, chain A/B, )
View:
Select:
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/B
A
16
P
2
UniProt
VAR_063768
T
83
M
GLYG_HUMAN
Disease (GSD15)
---
A/B
T
83
M
3
UniProt
VAR_072707
D
102
H
GLYG_HUMAN
Disease (PGBM2)
---
A/B
D
102
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3t7oa_ (A:)
1b: SCOP_d3t7ob_ (B:)
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Classes
(
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(
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(
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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
d3t7oa_
A:
1b
d3t7ob_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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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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Atom Selection
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all
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Protein
Nucleic
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Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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Asym.Unit (194 KB)
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