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PDBsum entry 6bpp
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Ligand/metal interactions
PDB id
6bpp
Ligand highlighted
PA1-GCS-KDO-GMH-
GMH-GLC-GLC-GLC-
GMH-KDO
Ligands
PA1-GCS-KDO-GMH-
GMH-GLC-GLC-GLC-
GMH-KDO
PA1 1(C) to KDO 10(C)
E1M
×2
E1M 601(A)
FTT
×4
FTT 602(A)
FTT 604(A)
FTT 614(B)
DAO
DAO 603(A)
3PE
×7
3PE 605(A)
3PE 606(A)
3PE 607(A)
3PE 608(A)
3PE 618(B)
3PE 619(B)
PO4
×2
PO4 612(B)
MYR
MYR 615(B)
Ligand
PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO
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
GCS
-
2-Amino-2-Deoxy-Beta-D-Glucopyranose [Beta-D-Glucosamine; 2-Amino-2-Deoxy-Beta-D-Glucose; 2- Amino-2-Deoxy-D-Glucose; 2-Amino-2-Deoxy-Glucose; d- Glucosamine]
Formula:
C
6
H
13
NO
5
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
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
GLC
-
Alpha-D-Glucopyranose [Alpha-D-Glucose; d-Glucose; glucose]
Formula:
C
6
H
12
O
6
Validation of ligand annotation
Per Residue Validation
Atoms
Missing
Incorrect Chiral Centres
Residue
Dic.
Struc.
Link
Subs.
Atoms
Rings
Planar
High
C
Other
PA1 1(C)
12
12
0
0
Complete
Chiral checks - OK
GCS 2(C)
12
12
1
0
Complete
Chiral checks - OK
KDO 3(C)
16
16
1
0
Complete
Chiral checks - OK
GMH 4(C)
14
14
1
0
Complete
Chiral checks - OK
GMH 5(C)
14
14
1
0
Complete
Chiral checks - OK
GLC 6(C)
12
12
1
0
Complete
Chiral checks - OK
GLC 7(C)
12
12
1
0
Complete
Chiral checks - OK
GLC 8(C)
12
12
1
0
Complete
Chiral checks - OK
GMH 9(C)
14
14
1
0
Complete
Chiral checks - OK
KDO 10(C)
16
16
1
0
Complete
Chiral checks - OK
Advanced Analysis
Residue
Name Mismatches
Count
PA1 1(C)
-
0
GCS 2(C)
-
0
KDO 3(C)
-
0
GMH 4(C)
-
0
GMH 5(C)
-
0
GLC 6(C)
-
0
GLC 7(C)
-
0
GLC 8(C)
-
0
GMH 9(C)
-
0
KDO 10(C)
O1B: O1A
|
O1A: O1B
2
Additional Information
Validation carried out using
MotiveValidator
. Full validation report can be found in
Validator
DB
.
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of interactions involving ligand PA1-GCS-KDO-GMH-GMH-GLC-GLC-GLC-GMH-KDO
List of
interactions
PA1 1(C) to KDO 10(C)
