SMTL ID : 7fio.1

LecA from Pseudomonas aeruginosa in complex with a synthetic monovalent galactosidic inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Y.36, D.100, T.104, N.107, N.108 Ligands: 4VH.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.36, A:D.100, A:T.104 CA.4: 6 residues within 4Å: Chain B: Y.36, D.100, T.104, N.107, N.108 Ligands: 4VH.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.36, B:D.100, B:T.104 CA.6: 6 residues within 4Å: Chain C: Y.36, D.100, T.104, N.107, N.108 Ligands: 4VH.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.36, C:D.100, C:T.104 CA.9: 6 residues within 4Å: Chain D: Y.36, D.100, T.104, N.107, N.108 Ligands: 4VH.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.36, D:D.100, D:T.104

4 x 4VH: N-[2-[4-[(2S)-3-(2-hydroxyethylamino)-3-oxidanylidene-2-(2-phenoxyethanoylamino)propyl]-1,2,3-triazol-1-yl]ethyl]-4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-benzamide(Non-covalent)

4VH.2: 12 residues within 4Å: Chain A: Y.36, E.49, H.50, P.51, Q.53, D.100, V.101, T.104, N.107 Chain B: T.39, Q.40 Ligands: CA.1 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:T.39, B:Q.40 Hydrogen bonds: A:E.49, A:Q.53, A:D.100, A:T.104, A:N.107 Water bridges: A:H.50, A:P.51 pi-Stacking: A:H.50 4VH.5: 9 residues within 4Å: Chain B: Y.36, H.50, Q.53, C.62, D.100, V.101, T.104, N.107 Ligands: CA.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.53, B:D.100, B:T.104, B:N.107 Water bridges: B:H.50, B:P.51, B:T.104, B:N.107 pi-Stacking: B:H.50 4VH.7: 8 residues within 4Å: Chain C: Y.36, H.50, Q.53, D.100, V.101, T.104, N.107 Ligands: CA.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.53, C:D.100, C:T.104, C:T.104, C:N.107 Water bridges: C:H.50, C:P.51, C:T.104, C:N.107 pi-Stacking: C:H.50 4VH.10: 12 residues within 4Å: Chain C: Q.40 Chain D: Y.36, E.49, H.50, P.51, Q.53, C.62, D.100, V.101, T.104, N.107 Ligands: CA.9 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:E.49 Hydrogen bonds: D:D.100, D:T.104, D:T.104, D:N.107, C:Q.40 Water bridges: D:H.50, D:P.51, D:T.104, D:N.107 pi-Stacking: D:H.50

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 1 residues within 4Å: Chain A: N.89 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain C: I.19, Y.20, N.21, P.22, Q.91, G.92 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.21 EDO.11: 3 residues within 4Å: Chain D: E.11, K.68, I.97 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.68 Water bridges: D:I.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Siebs, E. et al., Targeting the Central Pocket of the Pseudomonas aeruginosa Lectin LecA. Chembiochem (2022)

Release Date

2022-02-16

Peptides

PA-I galactophilic lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PA-I galactophilic lectin

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