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PDBsum entry 5vcs
Go to PDB code:
Ligand/metal interactions
PDB id
5vcs
2 instances of ligand highlighted
NAG-BMA-MAN-NAG-
MAN
Ligands
NAG-BMA-MAN-NAG-
MAN
×2
NAG 1(C) to MAN 5(C)
NAG 1(D) to MAN 5(D)
NAG
×2
NAG 501(A)
NAG 501(B)
DMS
×3
DMS 502(A)
DMS 503(A)
DMS 504(A)
PEG
PEG 502(B)
Ligand
NAG-BMA-MAN-NAG-MAN
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
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
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(C)
15
15
0
0
Complete
Chiral checks - OK
BMA 2(C)
12
12
1
0
Complete
Chiral checks - OK
MAN 3(C)
12
12
1
0
Complete
Chiral checks - OK
NAG 4(C)
15
15
1
0
Complete
Chiral checks - OK
MAN 5(C)
12
12
1
0
Complete
Chiral checks - OK
Additional Information
Validation carried out using
MotiveValidator
. Full validation report can be found in
Validator
DB
.
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3D Viewers:
Het Group NAG matches this enzyme's product UDP with similarity 42.86%
LIGPLOT
of interactions involving ligand NAG-BMA-MAN-NAG-MAN
List of
interactions
NAG 1(C) to MAN 5(C)
