SMTL ID : 5i8m.1

Bicyclic antimibrocial peptides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-tetramer

Ligands

1 x DLS- LYS- CYS- LYS- LEU- CYS- LEU- LYS- NH2: DLS-LYS-CYS-LYS-LEU-CYS-LEU-LYS-NH2(Non-covalent)

DLS-LYS-CYS-LYS-LEU-CYS-LEU-LYS-NH2.1: 11 residues within 4Å: Chain A: S.23, G.24 Chain C: T.36, A.37, A.38, T.39, F.40, G.51, T.52, Q.53 Ligands: ZDC.13 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.38, C:Q.53 Hydrogen bonds: C:T.39, C:T.39, C:T.39, C:T.52, C:T.52 Water bridges: A:D.96

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.95, D.99, D.101, D.104 Ligands: CA.3, ZDC.13 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.3: 7 residues within 4Å: Chain A: N.21, D.101, N.103, D.104 Chain D: G.114 Ligands: CA.2, ZDC.13 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Metal complexes: D:G.114, A:N.21, A:D.101, A:D.104 CA.4: 7 residues within 4Å: Chain A: G.114 Chain D: N.21, D.101, N.103, D.104 Ligands: ZDC.5, CA.12 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:N.21, D:D.101, D:D.104, A:G.114 CA.7: 6 residues within 4Å: Chain B: E.95, D.99, D.101, D.104 Ligands: ZDC.6, CA.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.95, B:D.99, B:D.99, B:D.101, B:D.104 CA.8: 8 residues within 4Å: Chain B: N.21, D.99, D.101, N.103, D.104 Chain C: G.114 Ligands: ZDC.6, CA.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:N.21, B:D.101, B:D.104, C:G.114 CA.9: 7 residues within 4Å: Chain B: G.114 Chain C: N.21, D.101, N.103, D.104 Ligands: ZDC.10, CA.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:N.21, C:D.101, C:D.104, B:G.114 CA.11: 6 residues within 4Å: Chain C: E.95, D.99, D.101, D.104 Ligands: CA.9, ZDC.10 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.95, C:E.95, C:D.99, C:D.101, C:D.104 CA.12: 6 residues within 4Å: Chain D: E.95, D.99, D.101, D.104 Ligands: CA.4, ZDC.5 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.95, D:D.99, D:D.101, D:D.104, D:D.104

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

ZDC.5: 11 residues within 4Å: Chain A: G.114 Chain D: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Ligands: CA.4, CA.12 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.23, D:S.23, D:D.104, A:G.114 ZDC.6: 12 residues within 4Å: Chain B: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain C: G.114 Ligands: CA.7, CA.8 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.23, B:S.23, C:G.114 Water bridges: B:T.98 ZDC.10: 12 residues within 4Å: Chain B: G.114 Chain C: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Ligands: CA.9, CA.11 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.23, C:S.23, C:D.104, C:D.104, B:G.114 ZDC.13: 13 residues within 4Å: Chain A: N.21, S.22, S.23, T.45, E.95, D.96, D.99, D.101, D.104 Chain D: G.114 Ligands: DLS-LYS-CYS-LYS-LEU-CYS-LEU-LYS-NH2.1, CA.2, CA.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:T.45 Hydrogen bonds: A:S.23, A:D.99, A:D.104, D:G.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Bonaventura, I. et al., Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms. Chem Sci (2017)

Release Date

2017-08-23

Peptides

Fucose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fucose-binding lectin

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