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PDBsum entry 2nyl
Go to PDB code:
Ligand/metal interactions
PDB id
2nyl
2 instances of ligand highlighted
DAL-LEU-ACB-ARG-
1ZN-FGA-DAM
Ligands
DAL-LEU-ACB-ARG-
1ZN-FGA-DAM
×2
DAL 1(G) to DAM 7(G)
Metals
_MN
×4
MN 502(C)
MN 501(C)
Ligand
DAL-LEU-ACB-ARG-1ZN-FGA-DAM
DAL
-
D-Alanine
Formula:
C
3
H
7
NO
2
ACB
-
3-Methyl-Beta-D-Aspartic acid [(3s)-3-Methyl-D-Aspartic acid; d-Methyl aspartic acid]
Formula:
C
5
H
9
NO
4
1ZN
-
(2s,3s,4e,6e,8s,9s)-3-Amino-9-Methoxy-2,6,8-Trimethyl- 10-Phenyldeca-4,6-Dienoic acid
Formula:
C
20
H
9
NO
3
FGA
-
Gamma-D-Glutamic acid [D-Glutamic acid]
Formula:
C
5
H
9
NO
4
DAM
-
N-Methyl-Alpha-Beta-Dehydroalanine
Formula:
C
4
H
7
NO
2
Validation of ligand annotation
Per Residue Validation
Atoms
Missing
Incorrect Chiral Centres
Residue
Dic.
Struc.
Link
Subs.
Atoms
Rings
Planar
High
C
Other
DAL 1(G)
-
-
-
-
Residue too small to validate
LEU 2(G)
-
-
-
-
Residue too small to validate
ACB 3(G)
-
-
-
-
Residue too small to validate
ARG 4(G)
-
-
-
-
Residue too small to validate
1ZN 5(G)
24
24
1
1
Complete
Chiral checks - OK
FGA 6(G)
-
-
-
-
Residue too small to validate
DAM 7(G)
-
-
-
-
Residue too small to validate
Advanced Analysis
Residue
Name Mismatches
Count
DAL 1(G)
-
0
LEU 2(G)
-
0
ACB 3(G)
-
0
ARG 4(G)
-
0
1ZN 5(G)
O3: OXT
1
FGA 6(G)
-
0
DAM 7(G)
-
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 DAL-LEU-ACB-ARG-1ZN-FGA-DAM
List of
interactions
DAL 1(G) to DAM 7(G)
(also representing equivalent ligand DAL 1(H) to DAM 7(H) )
_MN
×4
