SMTL ID : 6q8h.1

Structure of Fucosylated D-antimicrobial peptide SB10 in complex with the Fucose-binding lectin PA-IIL at 1.707 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

hetero-1-2-mer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.2, ZDC.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.95, A:E.95, A:D.99, A:D.101, A:D.104 CA.2: 6 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Ligands: CA.1, ZDC.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.21, A:D.101, A:D.104

2 x ZDC: 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid(Non-covalent)

ZDC.3: 14 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain B: L.3, K.4, A.5 Ligands: CA.1, CA.2, DLE.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:D.99, A:D.104 Water bridges: A:D.99 ZDC.6: 4 residues within 4Å: Chain C: L.3, K.4, A.5 Ligands: DLE.7 No protein-ligand interaction detected (PLIP)

2 x DLE: D-LEUCINE(Covalent)

DLE.4: 6 residues within 4Å: Chain A: S.23 Chain B: L.3, K.4, A.5, L.6 Ligands: ZDC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.23 DLE.7: 5 residues within 4Å: Chain C: L.3, K.4, A.5, L.6 Ligands: ZDC.6 No protein-ligand interaction detected (PLIP)

2 x NH2: AMINO GROUP(Non-functional Binders)

NH2.5: 4 residues within 4Å: Chain B: K.11, K.12, Y.13, K.14 No protein-ligand interaction detected (PLIP) NH2.8: 3 residues within 4Å: Chain C: A.10, K.11, K.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Baeriswyl, S. et al., X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes. Acs Chem.Biol. (2019)

Release Date

2019-03-20

Peptides

Fucose-binding lectin: A
SB10: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fucose-binding lectin

SB10

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