SMTL ID : 2jdh.1

Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-tetramer

Ligands

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

NAG-FUC.1: 13 residues within 4Å: Chain A: G.115 Chain B: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: TA5.7, CA.8, CA.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.24, B:D.97, B:D.100, B:D.102, B:S.24, B:D.97 Water bridges: B:T.99 NAG-FUC.2: 14 residues within 4Å: Chain C: N.22, S.23, S.24, T.46, E.96, D.97, G.98, D.100, D.102, D.105 Chain D: G.115 Ligands: CA.11, CA.12, TA5.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.46 Hydrogen bonds: C:S.24, C:D.97, C:D.100, C:D.102, C:S.24, C:D.97 Water bridges: C:S.24, C:T.99 NAG-FUC.3: 13 residues within 4Å: Chain C: G.115 Chain D: N.22, S.23, S.24, E.96, D.97, G.98, D.100, D.102, D.105 Ligands: TA5.14, CA.15, CA.16 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.24, D:D.97, D:D.100, D:D.105, C:G.115, D:S.24, D:D.97

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.4: 11 residues within 4Å: Chain A: N.22, S.23, S.24, E.96, D.97, D.100, D.102, D.105 Chain B: G.115 Ligands: CA.5, CA.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.24, A:D.97, A:D.102, A:D.105 Water bridges: A:E.96, A:D.97, A:D.100

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

CA.5: 7 residues within 4Å: Chain A: N.22, D.102, N.104, D.105 Chain B: G.115 Ligands: FUC.4, CA.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.22, A:D.102, A:D.105, B:G.115 CA.6: 6 residues within 4Å: Chain A: E.96, D.100, D.102, D.105 Ligands: FUC.4, 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.8: 6 residues within 4Å: Chain B: E.96, D.100, D.102, D.105 Ligands: NAG-FUC.1, CA.9 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.9: 7 residues within 4Å: Chain A: G.115 Chain B: N.22, D.102, N.104, D.105 Ligands: NAG-FUC.1, CA.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:G.115, B:N.22, B:D.102, B:D.105 CA.11: 7 residues within 4Å: Chain C: N.22, D.102, N.104, D.105 Chain D: G.115 Ligands: NAG-FUC.2, CA.12 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Metal complexes: D:G.115, C:N.22, C:D.102, C:D.105 CA.12: 6 residues within 4Å: Chain C: E.96, D.100, D.102, D.105 Ligands: NAG-FUC.2, CA.11 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.15: 7 residues within 4Å: Chain C: G.115 Chain D: N.22, D.102, N.104, D.105 Ligands: NAG-FUC.3, CA.16 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Metal complexes: C: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: NAG-FUC.3, 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

3 x TA5: 2H-1,2,3-TRIAZOL-4-YLMETHANOL(Non-covalent)(Non-functional Binders)

TA5.7: 1 residues within 4Å: Ligands: NAG-FUC.1 No protein-ligand interaction detected (PLIP) TA5.13: 1 residues within 4Å: Ligands: NAG-FUC.2 No protein-ligand interaction detected (PLIP) TA5.14: 1 residues within 4Å: Ligands: NAG-FUC.3 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-covalent)

SO4.10: 3 residues within 4Å: Chain C: S.45, T.46, N.47 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.46, C:T.46, C:T.46, C:N.47 Water bridges: C:Q.44, C:Q.44, C:S.45

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Marotte, K. et al., X-Ray Structures and Thermodynamics of the Interaction of Pa-Iil from Pseudomonas Aeruginosa with Disaccharide Derivatives. Chemmedchem (2007)

Release Date

2007-07-24

Peptides

FUCOSE-BINDING LECTIN PA-IIL: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

FUCOSE-BINDING LECTIN PA-IIL

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