SMTL ID : 5nf0.1

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 1.27 Å

Oligo State

hetero-4-3-mer

Ligands

1 x GLY: Fragment of ligand(Non-covalent)

GLY.1: 2 residues within 4Å: Chain A: S.23 Ligands: ZDC.5 Protein-ligand interaction information (PLIP) not available

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

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

ZDC.5: 12 residues within 4Å: Chain A: N.21, S.22, S.23, E.95, D.96, D.99, D.101, D.104 Chain C: G.114 Ligands: GLY.1, CA.2, CA.3 6 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: C:G.114, A:S.23, A:S.23, A:D.99, A:D.104 Water bridges: G.1 ZDC.9: 17 residues within 4Å: Chain B: N.21, S.22, S.23, T.45, E.95, D.96, G.97, D.99, D.101, D.104 Chain D: G.114 Chain E: C.1, K.6, K.7, K.8 Ligands: CA.6, CA.7 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:T.45 Hydrogen bonds: B:S.23, B:S.23, B:D.99, B:D.104, D:G.114 Water bridges: B:T.98 ZDC.11: 16 residues within 4Å: Chain A: G.114 Chain C: N.21, S.22, S.23, E.95, D.96, G.97, D.99, D.101, D.104 Chain G: C.1, K.6, C.11 Ligands: CA.4, CA.10, OXE.16 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.23, C:G.24, C:D.99, C:D.104, A:G.114 Water bridges: C:S.22, C:S.23 ZDC.13: 17 residues within 4Å: Chain B: G.114 Chain D: N.21, S.22, S.23, T.45, E.95, D.96, D.99, D.101, D.104 Chain F: C.1, K.6, K.7, K.8 Ligands: CA.8, CA.12, OXE.15 7 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: D:T.45, F:K.8 Hydrogen bonds: D:S.23, D:D.99, D:D.104, B:G.114 Water bridges: D:G.24

3 x OXE: ORTHO-XYLENE(Covalent)

OXE.14: 5 residues within 4Å: Chain B: V.69, N.70 Chain E: C.1, W.2, C.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.69 OXE.15: 7 residues within 4Å: Chain D: S.23, G.24 Chain F: C.1, W.2, W.10, C.11 Ligands: ZDC.13 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:W.10 OXE.16: 8 residues within 4Å: Chain C: R.72, D.96, G.97, T.98 Chain G: C.1, W.2, C.11 Ligands: ZDC.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:T.98, G:W.2, G:W.2

Links

RCSB   PDBe   PDBe-KB   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): ABCD
CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
G

G
H

Fucose-binding lectin II (PA-IIL)

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

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