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PDBsum entry 5kd7
Go to PDB code:
Ligand/metal interactions
PDB id
5kd7
4 instances of ligand highlighted
ILE-GLY-PRO-GLY-
ARG-ALA-PHE-TYR-
VAL
Ligands
ILE-GLY-PRO-GLY-
ARG-ALA-PHE-TYR-
VAL
×4
ILE 1(P) to VAL 9(P)
EDO
×7
EDO 301(A)
EDO 101(B)
EDO 102(B)
EDO 101(D)
EDO 302(F)
EDO 303(F)
EDO 301(I)
GOL
×2
GOL 301(F)
GOL 304(F)
Ligand
ILE-GLY-PRO-GLY-ARG-ALA-PHE-TYR-VAL
Validation of ligand annotation
Per Residue Validation
Atoms
Missing
Incorrect Chiral Centres
Residue
Dic.
Struc.
Link
Subs.
Atoms
Rings
Planar
High
C
Other
ILE 1(P)
9
9
1
1
Complete
Chiral checks - OK
GLY 2(P)
5
-
-
-
Residue too small to validate
PRO 3(P)
8
8
1
1
Complete
Chiral checks - OK
GLY 4(P)
5
-
-
-
Residue too small to validate
ARG 5(P)
12
12
1
1
Complete
Chiral checks - OK
ALA 6(P)
6
-
-
-
Residue too small to validate
PHE 7(P)
12
12
1
1
Complete
Chiral checks - OK
TYR 8(P)
13
13
1
1
Complete
Chiral checks - OK
VAL 9(P)
8
8
0
0
Complete
Chiral checks - OK
Advanced Analysis
Residue
Name Mismatches
Count
ILE 1(P)
-
0
GLY 2(P)
-
0
PRO 3(P)
-
0
GLY 4(P)
-
0
ARG 5(P)
-
0
ALA 6(P)
-
0
PHE 7(P)
O: OXT
1
TYR 8(P)
O: OXT
1
VAL 9(P)
OXT: O
|
O: OXT
2
Additional Information
Validation carried out using
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3D Viewers:
LIGPLOT
of interactions involving ligand ILE-GLY-PRO-GLY-ARG-ALA-PHE-TYR-VAL
List of
interactions
ILE 1(P) to VAL 9(P)
also representing 3 other equivalent ligands:
ILE 1(E) to VAL 9(E)
ILE 1(H) to VAL 9(H)
ILE 1(K) to VAL 9(K)
