SMTL ID : 5nes.1

Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-4-1-mer

Ligands

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

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

ZDC.4: 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.3, CA.12 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.23, D:S.23, D:D.99, D:D.104, D:D.104, A:G.114 Water bridges: D:D.99 ZDC.5: 14 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain B: C.1, W.2, W.3 Chain D: G.114 Ligands: CA.1, CA.2 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:S.23, A:S.23, A:D.99, A:D.104, D:G.114 Water bridges: B:W.2 ZDC.7: 11 residues within 4Å: Chain C: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain E: G.114 Ligands: CA.8, CA.9 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:G.114, C:S.23, C:S.23, C:D.99, C:D.104 ZDC.11: 11 residues within 4Å: Chain C: G.114 Chain E: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Ligands: CA.10, CA.13 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain E Hydrogen bonds: C:G.114, E:S.23, E:S.23, E:D.99, E:D.104 Water bridges: E:D.99

1 x 8VH: 1,3-dimethylbenzene(Covalent)

8VH.6: 4 residues within 4Å: Chain B: C.1, W.2, W.10, C.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.2, B:W.10, B:W.10 pi-Stacking: B:W.2

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

He, R. et al., Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa. Chem Sci (2017)

Release Date

2017-09-13

Peptides

Fucose-binding lectin II (PA-IIL): ACDE
CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

E
D

B
E

Fucose-binding lectin II (PA-IIL)

CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD

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