1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Live, D.
Borgert, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C8 H15 N O6
221.208
2-acetamido-2-deoxy-alpha-D-galactopyranose
N-acetyl-alpha-D-galactosamine; 2-acetamido-2-deoxy-alpha-D-galactose; 2-acetamido-2-deoxy-D-galactose; 2-acetamido-2-deoxy-galactose; N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
D-saccharide, alpha linking
C2 H4 O
44.053
ACETYL GROUP
non-polymer
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
UK
Glycobiology
9999
1460-2423
31
649
661
10.1093/glycob/cwaa112
33295623
Contrasting the conformational effects of alpha-O-GalNAc and alpha-O-Man glycan protein modifications and their impact on the mucin-like region of alpha-dystroglycan.
2021
0000-0003-2187-6872
10.2210/pdb2mk7/pdb
pdb_00002mk7
996.180
Alpha-dystroglycan
mucin domain peptide (UNP residues 419-427)
1
syn
polymer
221.208
2-acetamido-2-deoxy-alpha-D-galactopyranose
4
syn
non-polymer
Alpha-DG, aDG
no
yes
(ACE)PPTTTTKKP(NH2)
XPPTTTTKKPX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
Effects of O-GalNAc glycosylation on structure
atom_site
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_ref_seq_dif
struct_site
struct_site_gen
chem_comp
citation
citation_author
database_2
pdbx_database_status
repository
Initial release
Carbohydrate remediation
repository
Remediation
Atomic model
Data collection
Database references
Derived calculations
Structure summary
Database references
Structure summary
Other
1
0
2015-02-04
2
0
2020-07-29
2
1
2022-08-24
2
2
2023-06-14
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_chem_comp.pdbx_synonyms
_citation.country
_citation.journal_abbrev
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.year
_citation_author.identifier_ORCID
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
DGalpNAca
N-acetyl-a-D-galactopyranosamine
a-D-GalpNAc
GalNAc
BMRB
Y
RCSB
2014-02-02
REL
REL
REL
REL
A2G
2-acetamido-2-deoxy-alpha-D-galactopyranose
9606
human
Homo sapiens
sample
structures with the least restraint violations
50
16
2D 1H-1H NOESY
3D TOCSY-NOESY
2D 1H-15N HSQC
2D 1H-13C HSQC
2D 1H-1H TOCSY
2D 1H-1H COSY
2D 1H-13C HMBC
2-10
mM
2-10
mM
4.5
ambient
288
K
simulated annealing
1
closest to the average
2-10 mM aDG mucin domain peptide, 100% D2O
100% D2O
2-10 mM aDG mucin domain peptide, 95% H2O/5% D2O
95% H2O/5% D2O
Brunger A. T. et.al.
refinement
XPLOR-NIH
600
Varian
INOVA
Varian INOVA
800
Varian
INOVA
Varian INOVA
900
Varian
INOVA
Varian INOVA
A2G
12
2
A2G
A2G
101
A
A2G
13
2
A2G
A2G
102
A
A2G
14
2
A2G
A2G
103
A
A2G
15
2
A2G
A2G
104
A
ACE
1
n
1
ACE
1
A
PRO
2
n
2
PRO
2
A
PRO
3
n
3
PRO
3
A
THR
4
n
4
THR
4
A
THR
5
n
5
THR
5
A
THR
6
n
6
THR
6
A
THR
7
n
7
THR
7
A
LYS
8
n
8
LYS
8
A
LYS
9
n
9
LYS
9
A
PRO
10
n
10
PRO
10
A
NH2
11
n
11
NH2
11
A
author_defined_assembly
1
monomeric
A
THR
5
GLYCOSYLATION SITE
A
THR
5
THR
A
THR
7
GLYCOSYLATION SITE
A
THR
7
THR
A
THR
6
GLYCOSYLATION SITE
A
THR
6
THR
A
THR
4
GLYCOSYLATION SITE
A
THR
4
THR
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
2
A
PRO
3
-44.57
165.65
3
A
PRO
3
-44.52
91.55
3
A
LYS
9
19.98
74.08
4
A
PRO
3
-44.49
163.29
5
A
PRO
3
-44.56
105.17
5
A
LYS
8
42.91
96.21
7
A
PRO
3
-44.63
150.99
7
A
LYS
9
-175.82
46.65
8
A
PRO
3
-42.29
151.21
9
A
PRO
3
-42.59
156.73
10
A
PRO
3
-43.98
155.02
10
A
LYS
9
-175.86
46.55
11
A
PRO
3
-44.59
95.82
11
A
LYS
8
46.42
-146.92
11
A
LYS
9
21.39
61.31
12
A
PRO
3
-44.61
91.53
12
A
LYS
8
47.36
-176.98
12
A
LYS
9
-176.72
46.44
13
A
PRO
3
-46.37
98.87
14
A
PRO
3
-44.26
155.71
14
A
LYS
8
73.08
166.21
15
A
LYS
9
19.94
74.12
16
A
LYS
9
21.36
61.22
closest to the average, model1
Tetra-O-GalNAc glycosylated mucin sequence from alpha dystroglycan mucin domain
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
covale
1.305
both
A
ACE
1
A
C
ACE
1
1_555
A
PRO
2
A
N
PRO
2
1_555
covale
1.410
one
O-Glycosylation
A
THR
4
A
OG1
THR
4
1_555
A
A2G
101
B
C1
A2G
1_555
covale
1.410
one
O-Glycosylation
A
THR
5
A
OG1
THR
5
1_555
A
A2G
102
C
C1
A2G
1_555
covale
1.410
one
O-Glycosylation
A
THR
6
A
OG1
THR
6
1_555
A
A2G
103
D
C1
A2G
1_555
covale
1.410
one
O-Glycosylation
A
THR
7
A
OG1
THR
7
1_555
A
A2G
104
E
C1
A2G
1_555
covale
1.306
both
A
PRO
10
A
C
PRO
10
1_555
A
NH2
11
A
N
NH2
11
1_555
STRUCTURAL PROTEIN
mucin domain, glycoprotein, glycosylation, alpha-dystroglycan, Tn antigen, N-acetyl-galactosamine, STRUCTURAL PROTEIN
DAG1_HUMAN
UNP
1
419
Q14118
PPTTTTKKP
419
427
2MK7
2
10
Q14118
A
1
2
10
1
acetylation
ACE
1
2MK7
A
Q14118
UNP
1
1
amidation
NH2
11
2MK7
A
Q14118
UNP
11