SMTL ID : 1w8h.1

structure of pseudomonas aeruginosa lectin II (PA-IIL)complexed with lewisA trisaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- GAL- NDG- FUC: alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL-NDG-FUC.1: 12 residues within 4Å: Chain A: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Chain D: G.115 Ligands: CA.5, CA.6 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:G.115, A:S.24, A:D.97, A:D.100, A:D.100, A:S.24, A:D.97, A:D.97 Water bridges: A:D.100, A:D.100, A:S.24, A:S.24, A:S.24, A:S.24, A:T.99, A:T.99

2 x NAG- GAL- FUC: beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL-FUC.2: 13 residues within 4Å: Chain B: N.22, S.23, S.24, E.96, D.97, G.98, T.99, D.100, D.102, D.105 Chain C: G.115 Ligands: CA.10, CA.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.24, B:D.97, B:D.100, B:D.105, C:G.115, B:T.99, B:D.100, B:S.24, B:D.97 Water bridges: B:T.99, B:T.99, B:D.100, C:G.115 NAG-GAL-FUC.3: 12 residues within 4Å: Chain B: G.115 Chain C: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: CA.12, CA.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.24, C:D.97, C:D.100, C:D.102, C:D.105, C:D.100, C:S.24, C:G.25, C:D.97 Water bridges: C:T.99, C:D.100

1 x NDG- GAL- FUC: beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)

NDG-GAL-FUC.4: 12 residues within 4Å: Chain A: G.115 Chain D: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: CA.15, CA.16 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.115, D:S.24, D:D.97, D:D.100, D:D.100, D:S.24, D:D.97 Water bridges: D:D.100, D:D.100

8 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: N.22, D.102, N.104, D.105 Chain D: G.115 Ligands: NAG-GAL-NDG-FUC.1, CA.6 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Metal complexes: D:G.115, A:N.22, A:D.102, A:D.105 CA.6: 6 residues within 4Å: Chain A: E.96, D.100, D.102, D.105 Ligands: NAG-GAL-NDG-FUC.1, CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.96, A:E.96, A:D.100, A:D.102, A:D.105 CA.10: 7 residues within 4Å: Chain B: N.22, D.102, N.104, D.105 Chain C: G.115 Ligands: NAG-GAL-FUC.2, CA.11 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:N.22, B:D.102, B:D.105, C:G.115 CA.11: 6 residues within 4Å: Chain B: E.96, D.100, D.102, D.105 Ligands: NAG-GAL-FUC.2, CA.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.96, B:E.96, B:D.100, B:D.102, B:D.105 CA.12: 6 residues within 4Å: Chain C: E.96, D.100, D.102, D.105 Ligands: NAG-GAL-FUC.3, CA.13 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.96, C:E.96, C:D.100, C:D.102, C:D.105 CA.13: 7 residues within 4Å: Chain B: G.115 Chain C: N.22, D.102, N.104, D.105 Ligands: NAG-GAL-FUC.3, CA.12 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Metal complexes: B:G.115, C:N.22, C:D.102, C:D.105 CA.15: 7 residues within 4Å: Chain A: G.115 Chain D: N.22, D.102, N.104, D.105 Ligands: NDG-GAL-FUC.4, CA.16 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Metal complexes: A:G.115, D:N.22, D:D.102, D:D.105 CA.16: 6 residues within 4Å: Chain D: E.96, D.100, D.102, D.105 Ligands: NDG-GAL-FUC.4, CA.15 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.96, D:E.96, D:D.100, D:D.102, D:D.105

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain C: Q.44, S.45, N.47, A.49 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.45, C:N.47 Water bridges: C:T.46, C:T.46 SO4.8: 3 residues within 4Å: Chain A: A.39, T.40, Q.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.40, A:Q.54 Water bridges: A:T.40

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain C: T.3, Q.4, Q.65 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.4, C:Q.4 Water bridges: C:Q.65, C:D.76 GOL.14: 5 residues within 4Å: Chain C: A.38, A.39, T.40, F.41, Q.54 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.38, C:T.40, C:Q.54 Water bridges: C:T.40 GOL.17: 6 residues within 4Å: Chain B: A.2, Q.4, L.77 Chain D: A.2, Q.4, L.77 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:A.2, B:Q.4, D:A.2, D:D.76 Water bridges: B:L.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perret, S. et al., Structural Basis for the Interaction between Human Milk Oligosaccharides and the Bacterial Lectin Pa-Iil of Pseudomonas Aeruginosa. Biochem.J. (2005)

Release Date

2005-03-31

Peptides

PSEUDOMONAS AERUGINOSA LECTIN II: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PSEUDOMONAS AERUGINOSA LECTIN II

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