SMTL ID : 1w8f.1

PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LACTO-N-NEO- FUCOPENTAOSE V(LNPFV)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-tetramer

Ligands

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

BGC-GAL-NAG-FUC.1: 14 residues within 4Å: Chain A: N.22, S.23, S.24, T.46, E.96, D.97, G.98, T.99, D.100, D.102, D.105 Chain C: G.115 Ligands: CA.6, CA.7 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.24, A:D.97, A:S.24, A:D.97, A:D.100, A:D.105, C:G.115, A:T.99, A:D.100 Hydrophobic interactions: A:T.46 Water bridges: A:T.99, A:D.100

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

BGC-GAL-NAG-GAL-FUC.2: 14 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 D: G.115 Ligands: CA.9, CA.10, GOL.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.24, B:D.97, B:S.24, B:D.97, B:D.100, D:G.115 Water bridges: B:D.97, B:T.99 BGC-GAL-NAG-GAL-FUC.4: 14 residues within 4Å: Chain B: G.115 Chain D: N.22, S.23, S.24, E.96, D.97, G.98, T.99, D.100, D.102, D.105 Ligands: CA.16, CA.17, GOL.18 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.24, D:D.97, D:S.24, D:D.97, D:D.100, B:G.115 Water bridges: D:T.99

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

BGC-FUC-GAL.3: 14 residues within 4Å: Chain A: G.115 Chain C: N.22, S.23, S.24, R.73, E.96, D.97, G.98, T.99, D.100, D.102, D.105 Ligands: CA.13, CA.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.24, C:R.73, C:R.73, C:D.97, C:S.24, C:D.97, C:D.100, C:D.105, A:G.115, C:D.100 Water bridges: C:T.99, C:T.99

4 x SO4: SULFATE ION(Non-functional Binders)(Non-covalent)

SO4.5: 3 residues within 4Å: Chain A: S.45, T.46, N.47 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.46, A:T.46, A:T.46 Water bridges: A:Q.44, A:N.47, A:N.47 SO4.8: 4 residues within 4Å: Chain B: S.45, T.46, N.47, A.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.46, B:N.47 Water bridges: B:Q.44, B:Q.44 SO4.12: 4 residues within 4Å: Chain C: S.45, T.46, N.47, A.49 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.46, C:T.46, C:N.47, C:N.47 Water bridges: C:Q.44, C:Q.44 SO4.15: 2 residues within 4Å: Chain D: Q.44, T.46 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.44, D:T.46, D:T.46, D:T.46 Water bridges: D:N.47

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.6: 6 residues within 4Å: Chain A: E.96, D.100, D.102, D.105 Ligands: BGC-GAL-NAG-FUC.1, CA.7 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.7: 7 residues within 4Å: Chain A: N.22, D.102, N.104, D.105 Chain C: G.115 Ligands: BGC-GAL-NAG-FUC.1, CA.6 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Metal complexes: C:G.115, A:N.22, A:D.102, A:D.105 CA.9: 6 residues within 4Å: Chain B: E.96, D.100, D.102, D.105 Ligands: BGC-GAL-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.10: 7 residues within 4Å: Chain B: N.22, D.102, N.104, D.105 Chain D: G.115 Ligands: BGC-GAL-NAG-GAL-FUC.2, CA.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Metal complexes: B:N.22, B:D.102, B:D.105, D:G.115 CA.13: 6 residues within 4Å: Chain C: E.96, D.100, D.102, D.105 Ligands: BGC-FUC-GAL.3, CA.14 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.14: 7 residues within 4Å: Chain A: G.115 Chain C: N.22, D.102, N.104, D.105 Ligands: BGC-FUC-GAL.3, CA.13 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:N.22, C:D.102, C:D.105, A:G.115 CA.16: 6 residues within 4Å: Chain D: E.96, D.100, D.102, D.105 Ligands: BGC-GAL-NAG-GAL-FUC.4, CA.17 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 CA.17: 7 residues within 4Å: Chain B: G.115 Chain D: N.22, D.102, N.104, D.105 Ligands: BGC-GAL-NAG-GAL-FUC.4, CA.16 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:N.22, D:D.102, D:D.105, B:G.115

2 x GOL: GLYCEROL(Non-covalent)(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain B: D.100 Chain D: G.115 Ligands: BGC-GAL-NAG-GAL-FUC.2 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.115 GOL.18: 3 residues within 4Å: Chain B: G.115 Chain D: D.100 Ligands: BGC-GAL-NAG-GAL-FUC.4 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:N.104, B:L.114

Links

RCSB   PDBe   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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