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PDBsum entry 5ydh
Go to PDB code:
Ligand/metal interactions
PDB id
5ydh
Ligand highlighted
NAG-NAG-BMA-MAN-
MAN
Ligands
NAG-NAG-BMA-MAN
NAG 1(C) to MAN 4(C)
NAG-NAG-BMA-MAN-
MAN
NAG 1(D) to MAN 5(D)
SO4
×26
SO4 801(A)
SO4 802(A)
SO4 803(A)
SO4 804(A)
SO4 805(A)
SO4 807(A)
SO4 808(A)
SO4 809(A)
SO4 810(A)
SO4 804(B)
SO4 809(B)
SO4 810(B)
SO4 811(B)
SO4 812(B)
SO4 814(B)
SO4 816(B)
NAG
×2
NAG 811(A)
EPE
×3
EPE 812(A)
EPE 813(A)
GOL
×3
GOL 814(A)
GOL 815(A)
Metals
_CO
×2
CO 816(A)
Ligand
NAG-NAG-BMA-MAN-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(D)
15
15
1
1
Complete
Chiral checks - OK
NAG 2(D)
15
15
1
0
Complete
Chiral checks - OK
BMA 3(D)
12
12
1
0
Complete
Chiral checks - OK
MAN 4(D)
12
12
1
0
Complete
Chiral checks - OK
MAN 5(D)
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:
LIGPLOT
of interactions involving ligand NAG-NAG-BMA-MAN-MAN
List of
interactions
NAG 1(D) to MAN 5(D)
_CO
×2
