SMTL ID : 5dkp.2 (1 other biounit)

Crystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-14-mer

Ligands

14 x OTT- PHE- SER- PRO- MAA- ALA- MP8: agonist ADEP A54556(Non-covalent)

OTT-PHE-SER-PRO-MAA-ALA-MP8.1: 15 residues within 4Å: Chain A: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, F.119, L.121, L.198 Chain G: L.55, S.59, T.86, F.89 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:R.29, A:L.30, A:L.30, A:E.33, A:F.67, A:F.67, A:Y.69, A:L.97, A:F.119, A:L.121, A:L.198, G:L.55, G:L.55, G:T.86 Hydrogen bonds: A:Y.69, A:Y.69 pi-Stacking: G:F.89 OTT-PHE-SER-PRO-MAA-ALA-MP8.2: 16 residues within 4Å: Chain A: L.55, S.59, T.86, F.89 Chain B: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:R.29, B:L.30, B:E.33, B:E.33, B:F.67, B:F.67, B:Y.69, B:L.97, B:L.97, B:L.99, B:F.119, B:L.121, B:L.121, B:L.198, A:L.55, A:L.55, A:F.89 Hydrogen bonds: B:Y.69, B:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.3: 14 residues within 4Å: Chain B: L.55, F.56, S.59, T.86, F.89 Chain C: R.29, L.30, E.33, I.35, F.67, Y.69, F.119, L.121, L.198 16 PLIP interactions: 4 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:L.55, B:L.55, B:F.89, C:R.29, C:L.30, C:E.33, C:I.35, C:F.67, C:Y.69, C:F.119, C:L.121, C:L.121, C:L.198 Water bridges: B:E.58 Hydrogen bonds: C:Y.69, C:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.4: 17 residues within 4Å: Chain C: L.55, F.56, S.59, T.86, F.89 Chain D: R.29, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 Ligands: NA.18 17 PLIP interactions: 2 interactions with chain C, 15 interactions with chain D Hydrophobic interactions: C:L.55, D:R.29, D:E.33, D:E.33, D:I.35, D:F.67, D:F.67, D:Y.69, D:L.97, D:L.97, D:L.99, D:F.119, D:L.121, D:L.121 pi-Stacking: C:F.89 Hydrogen bonds: D:Y.69, D:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.5: 17 residues within 4Å: Chain D: L.55, F.56, S.59, T.86, F.89 Chain E: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 19 PLIP interactions: 15 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:R.29, E:L.30, E:E.33, E:E.33, E:I.35, E:F.67, E:F.67, E:Y.69, E:L.97, E:L.99, E:F.119, E:L.121, E:L.198, D:L.55, D:L.55, D:F.56, D:F.89 Hydrogen bonds: E:Y.69, E:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.6: 15 residues within 4Å: Chain E: L.55, F.56, S.59, T.86, F.89 Chain F: R.29, L.30, E.33, I.35, F.67, Y.69, L.97, F.119, L.121, L.198 16 PLIP interactions: 3 interactions with chain E, 13 interactions with chain F Hydrophobic interactions: E:F.56, E:T.86, E:F.89, F:R.29, F:L.30, F:L.30, F:E.33, F:F.67, F:Y.69, F:L.97, F:F.119, F:L.121, F:L.121, F:L.198 Hydrogen bonds: F:Y.69, F:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.7: 17 residues within 4Å: Chain F: L.55, F.56, S.59, T.86, F.89 Chain G: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 19 PLIP interactions: 5 interactions with chain F, 14 interactions with chain G Hydrophobic interactions: F:L.55, F:L.55, F:F.56, F:F.89, F:F.89, G:R.29, G:L.30, G:L.30, G:E.33, G:F.67, G:F.67, G:Y.69, G:L.99, G:F.119, G:L.121, G:L.121, G:L.198 Hydrogen bonds: G:Y.69, G:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.8: 13 residues within 4Å: Chain H: R.29, E.33, I.35, F.67, Y.69, L.97, F.119, L.121, L.198 Chain N: L.55, S.59, T.86, F.89 14 PLIP interactions: 9 interactions with chain H, 5 interactions with chain N Hydrophobic interactions: H:E.33, H:F.67, H:Y.69, H:L.97, H:F.119, H:L.121, H:L.198, N:L.55, N:L.55, N:T.86, N:F.89 Hydrogen bonds: H:Y.69, H:Y.69 Water bridges: N:E.58 OTT-PHE-SER-PRO-MAA-ALA-MP8.9: 16 residues within 4Å: Chain H: L.55, F.56, S.59, T.86, F.89 Chain I: R.29, L.30, E.33, I.35, F.67, Y.69, L.97, F.119, L.121, L.198 Ligands: NA.24 13 PLIP interactions: 10 interactions with chain I, 3 interactions with chain H Hydrophobic interactions: I:R.29, I:L.30, I:F.67, I:Y.69, I:L.97, I:L.121, I:L.121, I:L.198, H:L.55, H:F.89 Hydrogen bonds: I:Y.69, I:Y.69 Water bridges: H:E.58 OTT-PHE-SER-PRO-MAA-ALA-MP8.10: 15 residues within 4Å: Chain I: L.55, S.59, T.86, F.89 Chain J: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, F.119, L.121, L.198 18 PLIP interactions: 15 interactions with chain J, 3 interactions with chain I Hydrophobic interactions: J:R.29, J:L.30, J:L.30, J:E.33, J:I.35, J:F.67, J:F.67, J:Y.69, J:L.97, J:F.119, J:L.121, J:L.121, J:L.198, I:L.55, I:L.55, I:F.89 Hydrogen bonds: J:Y.69, J:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.11: 16 residues within 4Å: Chain J: L.55, S.59, T.86, F.89 Chain K: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, F.119, L.121, L.198, R.201 17 PLIP interactions: 13 interactions with chain K, 4 interactions with chain J Hydrophobic interactions: K:R.29, K:L.30, K:L.30, K:E.33, K:F.67, K:F.67, K:Y.69, K:L.97, K:L.121, K:L.121, K:L.198, J:L.55, J:L.55, J:L.55 Hydrogen bonds: K:Y.69, K:Y.69 pi-Stacking: J:F.89 OTT-PHE-SER-PRO-MAA-ALA-MP8.12: 18 residues within 4Å: Chain K: L.55, F.56, S.59, T.86, F.89 Chain L: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 Ligands: NA.28 16 PLIP interactions: 3 interactions with chain K, 13 interactions with chain L Hydrophobic interactions: K:L.55, K:F.56, L:L.30, L:E.33, L:E.33, L:I.35, L:F.67, L:F.67, L:Y.69, L:L.97, L:L.99, L:L.121, L:L.121 pi-Stacking: K:F.89 Hydrogen bonds: L:Y.69, L:Y.69 OTT-PHE-SER-PRO-MAA-ALA-MP8.13: 16 residues within 4Å: Chain L: L.55, S.59, T.86, F.89 Chain M: R.29, L.30, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 17 PLIP interactions: 13 interactions with chain M, 4 interactions with chain L Hydrophobic interactions: M:E.33, M:E.33, M:F.67, M:F.67, M:Y.69, M:L.97, M:L.99, M:F.119, M:L.121, M:L.121, M:L.198, L:L.55, L:L.55, L:L.55 Hydrogen bonds: M:Y.69, M:Y.69 pi-Stacking: L:F.89 OTT-PHE-SER-PRO-MAA-ALA-MP8.14: 16 residues within 4Å: Chain M: L.55, F.56, S.59, T.86, F.89 Chain N: L.30, E.33, I.35, F.67, Y.69, S.95, L.97, L.99, F.119, L.121, L.198 14 PLIP interactions: 10 interactions with chain N, 4 interactions with chain M Hydrophobic interactions: N:L.30, N:F.67, N:F.67, N:Y.69, N:L.97, N:L.99, N:F.119, N:L.121, M:L.55, M:F.56, M:F.89 Hydrogen bonds: N:Y.69, N:Y.69 Water bridges: M:E.58

14 x K: POTASSIUM ION(Non-covalent)

K.15: 3 residues within 4Å: Chain A: M.87, I.90, P.92 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.87, A:I.90, A:P.92, H2O.1 K.16: 3 residues within 4Å: Chain B: M.87, I.90, P.92 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.87, B:I.90, B:P.92, H2O.2, H2O.2 K.17: 4 residues within 4Å: Chain C: M.87, I.90, K.91, P.92 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:M.87, C:I.90, H2O.3, H2O.3, H2O.3 K.19: 3 residues within 4Å: Chain D: M.87, I.90, P.92 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:M.87, D:I.90, D:P.92, H2O.4, H2O.4 K.20: 3 residues within 4Å: Chain E: M.87, I.90, P.92 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:M.87, E:P.92, H2O.5, H2O.6 K.21: 4 residues within 4Å: Chain F: M.87, I.90, K.91, P.92 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:M.87, F:I.90, F:P.92 K.22: 3 residues within 4Å: Chain G: M.87, I.90, P.92 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:M.87, G:I.90, G:P.92, H2O.7, H2O.8 K.23: 3 residues within 4Å: Chain H: M.87, I.90, P.92 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:M.87, H:I.90, H:P.92, H2O.9 K.25: 3 residues within 4Å: Chain I: M.87, I.90, P.92 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:M.87, I:I.90, I:P.92, H2O.9, H2O.9 K.26: 3 residues within 4Å: Chain J: M.87, I.90, P.92 5 PLIP interactions: 2 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:M.87, J:I.90, H2O.10, H2O.10, H2O.11 K.27: 3 residues within 4Å: Chain K: M.87, I.90, P.92 5 PLIP interactions: 2 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:M.87, K:I.90, H2O.11, H2O.12, H2O.12 K.29: 3 residues within 4Å: Chain L: M.87, I.90, P.92 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:M.87, L:P.92, H2O.13, H2O.13 K.30: 3 residues within 4Å: Chain M: M.87, I.90, P.92 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:M.87, M:I.90, M:P.92, H2O.14 K.31: 3 residues within 4Å: Chain N: M.87, I.90, P.92 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:M.87, N:I.90, N:P.92, H2O.15

3 x NA: SODIUM ION(Non-functional Binders)

NA.18: 4 residues within 4Å: Chain C: E.58, F.89, I.90 Ligands: OTT-PHE-SER-PRO-MAA-ALA-MP8.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.58 NA.24: 3 residues within 4Å: Chain H: E.58, F.89 Ligands: OTT-PHE-SER-PRO-MAA-ALA-MP8.9 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.58 NA.28: 4 residues within 4Å: Chain K: E.58, F.89 Ligands: OTT-PHE-SER-PRO-MAA-ALA-MP8.12, OTT-PHE-SER-PRO-MAA-ALA-MP8.12 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodreid, J.D. et al., Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J.Med.Chem. (2016)

Release Date

2016-01-27

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

B
b

C
c

D
d

E
e

F
f

G
g

H
h

I
i

J
j

K
k

L
l

M
m

N
n

ATP-dependent Clp protease proteolytic subunit

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