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PDBsum entry 3v0w
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Ligand/metal interactions
PDB id
3v0w
Ligand highlighted
KDO-GM0-GM0-GLC-
GLC-GLC-PA1-GLA-
GMH-KDO
Ligands
KDO-GM0-GM0-GLC-
GLC-GLC-PA1-GLA-
GMH-KDO
KDO 1(A) to KDO 10(A)
SO4
×10
SO4 301(L)
SO4 302(L)
SO4 303(L)
SO4 304(L)
SO4 311(H)
SO4 312(H)
SO4 313(H)
SO4 314(H)
SO4 315(H)
SO4 316(H)
Ligand
KDO-GM0-GM0-GLC-GLC-GLC-PA1-GLA-GMH-KDO
KDO
-
3-Deoxy-Alpha-D-Manno-Oct-2-Ulopyranosonic acid [3-Deoxy-D-Manno-Oct-2-Ulopyranosonic acid; 2-Keto-3- Deoxy-D-Mannooctanoic acid; 3-Deoxy-Alpha-D-Manno-Oct- 2-Ulosonic acid; 3-Deoxy-D-Manno-Oct-2-Ulosonic acid; 3-Deoxy-Manno-Oct-2-Ulosonic acid]
Formula:
C
8
H
14
O
8
GM0
-
4-O-Phosphono-L-Glycero-Alpha-D-Manno-Heptopyranose [4-O-Phosphono-L-Glycero-Alpha-D-Manno-Heptose; 4-O- Phosphono-L-Glycero-D-Manno-Heptose; 4-O-Phosphono-L- Glycero-Manno-Heptose]
Formula:
C
7
HOO
10
P
GLC
-
Alpha-D-Glucopyranose [Alpha-D-Glucose; d-Glucose; glucose]
Formula:
C
6
H
12
O
6
PA1
-
2-Amino-2-Deoxy-Alpha-D-Glucopyranose [Alpah-D-Glucosamine; 2-Amino-2-Deoxy-Alpha-D-Glucose; 2-Amino-2-Deoxy-D-Glucose; 2-Amino-2-Deoxy-Glucose]
Formula:
C
6
H
13
NO
5
GLA
-
Alpha-D-Galactopyranose [Alpha-D-Galactose; d-Galactose; galactose; alpha d- Galactose]
Formula:
C
6
H
12
O
6
GMH
-
L-Glycero-Alpha-D-Manno-Heptopyranose [L-Glycero-Alpha-D-Manno-Heptose; l-Glycero-D-Manno- Heptose; l-Glycero-Manno-Heptose; l-Glycero-D-Manno- Heptopyranose]
Formula:
C
7
H
14
O
7
Validation of ligand annotation
Per Residue Validation
Atoms
Missing
Incorrect Chiral Centres
Residue
Dic.
Struc.
Link
Subs.
Atoms
Rings
Planar
High
C
Other
KDO 1(A)
16
16
0
0
Complete
Chiral checks - OK
GM0 2(A)
18
18
1
0
Complete
Chiral checks - OK
GM0 3(A)
18
18
1
0
Complete
Chiral checks - OK
GLC 4(A)
12
12
1
0
Complete
Chiral checks - OK
GLC 5(A)
12
12
1
0
Complete
Chiral checks - OK
GLC 6(A)
12
12
1
0
Complete
Chiral checks - OK
PA1 7(A)
12
12
1
0
Complete
Chiral checks - OK
GLA 8(A)
12
12
1
0
Complete
Chiral checks - OK
GMH 9(A)
14
14
1
0
Complete
Chiral checks - OK
KDO 10(A)
16
16
1
0
Complete
Chiral checks - OK
Advanced Analysis
Residue
Name Mismatches
Count
KDO 1(A)
O1B: O1A
|
O1A: O1B
2
GM0 2(A)
-
0
GM0 3(A)
O8: O1A
|
O9: O8
|
O1A: O9
3
GLC 4(A)
-
0
GLC 5(A)
-
0
GLC 6(A)
-
0
PA1 7(A)
-
0
GLA 8(A)
-
0
GMH 9(A)
-
0
KDO 10(A)
-
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 KDO-GM0-GM0-GLC-GLC-GLC-PA1-GLA-GMH-KDO
List of
interactions
KDO 1(A) to KDO 10(A)
