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PDBsum entry 3v8x
Go to PDB code:
Ligand/metal interactions
PDB id
3v8x
Ligand highlighted
NAG-NAG-BMA-MAN-
NAG-GAL-SIA-MAN-
NAG
Ligands
NAG-NAG-BMA-MAN-
NAG-GAL-SIA-MAN-
NAG-GAL
NAG 1(C) to GAL 10(C)
NAG-NAG-BMA-MAN-
NAG-GAL-SIA-MAN-
NAG
NAG 1(D) to NAG 9(D)
C8E
×2
C8E 1001(A)
C8E 1002(A)
Ligand
NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG
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
GAL
-
Beta-D-Galactopyranose [Beta-D-Galactose; d-Galactose; galactose]
Formula:
C
6
H
12
O
6
SIA
-
N-Acetyl-Alpha-Neuraminic acid [N-Acetylneuraminic acid; sialic acid; alpha-Sialic acid; o-Sialic acid]
Formula:
C
11
H
9
NO
9
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
NAG 5(D)
15
15
1
0
Complete
Chiral checks - OK
GAL 6(D)
12
12
1
0
Complete
Chiral checks - OK
SIA 7(D)
21
21
1
0
Complete
Chiral checks - OK
MAN 8(D)
12
12
1
0
Complete
Chiral checks - OK
NAG 9(D)
15
15
1
0
Complete
Chiral checks - OK
Advanced Analysis
Residue
Name Mismatches
Count
NAG 1(D)
-
0
NAG 2(D)
-
0
BMA 3(D)
-
0
MAN 4(D)
-
0
NAG 5(D)
-
0
GAL 6(D)
-
0
SIA 7(D)
O1B: O1A
|
O1A: O1B
2
MAN 8(D)
-
0
NAG 9(D)
-
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-NAG-BMA-MAN-NAG-GAL-SIA-MAN-NAG
List of
interactions
NAG 1(D) to NAG 9(D)
