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PDBsum entry 5j5j
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Ligand/metal interactions
PDB id
5j5j
Ligand highlighted
NAG-NAG-BMA-MAN-
MAN-FUC
Ligands
NAG-NAG-BMA-MAN-
NAG-GAL-MAN-NAG
NAG 1(B) to NAG 8(B)
NAG-NAG-BMA-MAN-
MAN-FUC
NAG 1(C) to FUC 6(C)
NAG-NAG
NAG 1(D) to NAG 2(D)
MAN
×3
MAN 609(A)
MAN 610(A)
MAN 611(A)
NAG
×2
NAG 620(A)
NAG 621(A)
Metals
_CL
×2
CL 634(A)
CL 633(A)
_CA
×11
CA 622(A)
CA 623(A)
CA 624(A)
CA 625(A)
CA 626(A)
CA 627(A)
CA 628(A)
CA 629(A)
CA 630(A)
CA 631(A)
CA 632(A)
Ligand
NAG-NAG-BMA-MAN-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
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(C)
15
15
1
1
Complete
Chiral checks - OK
NAG 2(C)
15
15
1
0
Complete
Chiral checks - OK
BMA 3(C)
12
12
1
0
Complete
Chiral checks - OK
MAN 4(C)
12
12
1
0
Complete
Chiral checks - OK
MAN 5(C)
12
12
1
0
Complete
Chiral checks - OK
FUC 6(C)
11
11
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-FUC
List of
interactions
NAG 1(C) to FUC 6(C)
_CL
×2
_CA
×11
