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PDBsum entry 1rd3
Go to PDB code:
Ligand/metal interactions
PDB id
1rd3
Ligand highlighted
NAG-NDG-BMA-MAN-
FUC
Ligands
NAG-NDG-BMA-MAN-
FUC
NAG 1(E) to FUC 5(E)
NAG-NDG-FUC
NAG 1(F) to FUC 3(F)
PO4
×3
PO4 248(B)
PO4 249(B)
GOL
×6
GOL 250(B)
GOL 251(B)
GOL 252(B)
GOL 253(B)
GOL 254(B)
GOL 249(D)
Ligand
NAG-NDG-BMA-MAN-FUC
NAG
-
2-Acetamido-2-Deoxy-Beta-D-Glucopyranose [N-Acetyl-Beta-D-Glucosamine; 2-Acetamido-2-Deoxy-Beta- D-Glucose; 2-Acetamido-2-Deoxy-D-Glucose; 2-Acetamido- 2-Deoxy-Glucose; n-Acetyl-D-Glucosamine]
Formula:
C
8
H
15
NO
6
NDG
-
2-Acetamido-2-Deoxy-Alpha-D-Glucopyranose [N-Acetyl-Alpha-D-Glucosamine; 2-Acetamido-2-Deoxy- Alpha-D-Glucose; 2-Acetamido-2-Deoxy-D-Glucose; 2- Acetamido-2-Deoxy-Glucose; 2-(Acetylamino)-2-Deoxy-A- D-Glucopyranose]
Formula:
C
8
H
15
NO
6
BMA
-
Beta-D-Mannopyranose [Beta-D-Mannose; d-Mannose; mannose]
Formula:
C
6
H
12
O
6
MAN
-
Alpha-D-Mannopyranose [Alpha-D-Mannose; d-Mannose; mannose]
Formula:
C
6
H
12
O
6
FUC
-
Alpha-L-Fucopyranose [Alpha-L-Fucose; 6-Deoxy-Alpha-L-Galactopyranose; l- Fucose; fucose]
Formula:
C
6
H
12
O
5
Validation of ligand annotation
Per Residue Validation
Atoms
Missing
Incorrect Chiral Centres
Residue
Dic.
Struc.
Link
Subs.
Atoms
Rings
Planar
High
C
Other
NAG 1(E)
15
15
1
1
0
0
0
0
1
0
NDG 2(E)
15
15
1
0
0
0
0
0
0
0
BMA 3(E)
12
12
1
0
0
0
0
0
0
0
MAN 4(E)
12
12
1
0
0
0
0
0
0
0
FUC 5(E)
11
11
1
0
0
0
0
0
0
0
Additional Information
Validation carried out using
MotiveValidator
. Full validation report can be found in
Validator
DB
.
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3D Viewers:
LIGPLOT
of interactions involving ligand NAG-NDG-BMA-MAN-FUC
List of
interactions
NAG 1(E) to FUC 5(E)
