SMTL ID : 6nah.1 (1 other biounit)

Crystal structure of Neisseria meningitidis ClpP protease in complex with Acyldepsipeptide-14 (ADEP-14)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-14-mer

Ligands

14 x WFP- ALO- PRO- YCP- ALA- MP8: Acyldepsipeptide-14(Non-covalent)

WFP-ALO-PRO-YCP-ALA-MP8.1: 16 residues within 4Å: Chain A: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, Q.207, L.209 Chain G: V.62, L.66, D.96, T.97, F.100 Ligands: OCA.8 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:I.46, A:F.78, A:F.78, A:Y.80, A:L.108, A:F.130, A:F.130, A:L.132, A:L.132, A:L.209, A:L.209, G:F.100 Hydrogen bonds: A:Y.80 Halogen bonds: G:D.96 WFP-ALO-PRO-YCP-ALA-MP8.2: 15 residues within 4Å: Chain A: V.62, L.66, D.96, T.97, F.100 Chain B: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.9 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B pi-Stacking: A:F.100 Halogen bonds: A:D.96 Hydrophobic interactions: B:E.44, B:I.46, B:F.78, B:F.78, B:Y.80, B:L.108, B:F.130, B:F.130, B:L.132, B:L.132, B:L.209 Hydrogen bonds: B:Y.80 WFP-ALO-PRO-YCP-ALA-MP8.3: 15 residues within 4Å: Chain B: V.62, L.66, D.96, T.97, F.100 Chain C: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.10 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.44, C:F.78, C:F.78, C:Y.80, C:L.108, C:F.130, C:F.130, C:L.132, C:L.132, C:L.209, C:L.209, B:T.97 Hydrogen bonds: C:Y.80 pi-Stacking: B:F.100 Halogen bonds: B:D.96 WFP-ALO-PRO-YCP-ALA-MP8.4: 15 residues within 4Å: Chain C: V.62, L.66, D.96, T.97, F.100 Chain D: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.11 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:E.44, D:I.46, D:F.78, D:Y.80, D:L.108, D:F.130, D:F.130, D:L.132, D:L.132, D:L.209, C:F.100 Hydrogen bonds: D:Y.80 Halogen bonds: C:D.96 WFP-ALO-PRO-YCP-ALA-MP8.5: 16 residues within 4Å: Chain D: V.62, L.66, D.96, T.97, F.100 Chain E: E.44, I.46, F.78, Y.80, S.106, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.12 15 PLIP interactions: 3 interactions with chain D, 12 interactions with chain E Hydrophobic interactions: D:T.97, D:F.100, E:E.44, E:I.46, E:F.78, E:F.78, E:Y.80, E:L.108, E:F.130, E:F.130, E:L.132, E:L.132, E:L.209 Halogen bonds: D:D.96 Hydrogen bonds: E:Y.80 WFP-ALO-PRO-YCP-ALA-MP8.6: 15 residues within 4Å: Chain E: V.62, L.66, D.96, T.97, F.100 Chain F: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.13 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:E.44, F:I.46, F:F.78, F:F.78, F:Y.80, F:L.108, F:F.130, F:F.130, F:L.132, F:L.132, F:L.209, F:L.209 Hydrogen bonds: F:Y.80 pi-Stacking: E:F.100 Halogen bonds: E:D.96 WFP-ALO-PRO-YCP-ALA-MP8.7: 14 residues within 4Å: Chain F: V.62, L.66, D.96, T.97, F.100 Chain G: E.44, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.14 13 PLIP interactions: 3 interactions with chain F, 10 interactions with chain G Hydrophobic interactions: F:T.97, G:E.44, G:F.78, G:F.78, G:Y.80, G:L.108, G:F.130, G:F.130, G:L.132, G:L.209 pi-Stacking: F:F.100 Halogen bonds: F:D.96 Hydrogen bonds: G:Y.80 WFP-ALO-PRO-YCP-ALA-MP8.15: 15 residues within 4Å: Chain H: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Chain N: V.62, L.66, D.96, T.97, F.100 Ligands: OCA.22 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain N Hydrophobic interactions: H:E.44, H:I.46, H:F.78, H:F.78, H:F.78, H:Y.80, H:L.108, H:F.130, H:F.130, H:L.132, H:L.132, H:L.209, H:L.209, N:F.100 Hydrogen bonds: H:Y.80 WFP-ALO-PRO-YCP-ALA-MP8.16: 15 residues within 4Å: Chain H: V.62, L.66, D.96, T.97, F.100 Chain I: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.23 15 PLIP interactions: 13 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:E.44, I:I.46, I:F.78, I:F.78, I:Y.80, I:L.108, I:F.130, I:F.130, I:L.132, I:L.132, I:L.209, I:L.209 Hydrogen bonds: I:Y.80 pi-Stacking: H:F.100 Halogen bonds: H:D.96 WFP-ALO-PRO-YCP-ALA-MP8.17: 15 residues within 4Å: Chain I: V.62, L.66, D.96, T.97, F.100 Chain J: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.24 14 PLIP interactions: 12 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:E.44, J:I.46, J:F.78, J:F.78, J:Y.80, J:L.108, J:F.130, J:F.130, J:L.132, J:L.132, J:L.209, I:F.100 Hydrogen bonds: J:Y.80 Halogen bonds: I:D.96 WFP-ALO-PRO-YCP-ALA-MP8.18: 15 residues within 4Å: Chain J: V.62, L.66, D.96, T.97, F.100 Chain K: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.25 13 PLIP interactions: 11 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:E.44, K:F.78, K:Y.80, K:L.108, K:F.130, K:F.130, K:F.130, K:L.132, K:L.132, K:L.209, J:F.100 Hydrogen bonds: K:Y.80 Halogen bonds: J:D.96 WFP-ALO-PRO-YCP-ALA-MP8.19: 15 residues within 4Å: Chain K: V.62, L.66, D.96, T.97, F.100 Chain L: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.26 14 PLIP interactions: 12 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:E.44, L:I.46, L:F.78, L:Y.80, L:L.108, L:F.130, L:F.130, L:F.130, L:L.132, L:L.209, L:L.209, K:F.100 Hydrogen bonds: L:Y.80 Halogen bonds: K:D.96 WFP-ALO-PRO-YCP-ALA-MP8.20: 13 residues within 4Å: Chain L: L.66, D.96, T.97, F.100 Chain M: E.44, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.27 15 PLIP interactions: 3 interactions with chain L, 12 interactions with chain M Hydrophobic interactions: L:F.100, L:F.100, M:E.44, M:F.78, M:F.78, M:Y.80, M:L.108, M:F.130, M:F.130, M:L.132, M:L.132, M:L.209, M:L.209 Halogen bonds: L:D.96 Hydrogen bonds: M:Y.80 WFP-ALO-PRO-YCP-ALA-MP8.21: 15 residues within 4Å: Chain M: V.62, L.66, D.96, T.97, F.100 Chain N: E.44, I.46, F.78, Y.80, L.108, L.110, F.130, L.132, L.209 Ligands: OCA.28 14 PLIP interactions: 12 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:E.44, N:I.46, N:F.78, N:Y.80, N:L.108, N:L.110, N:F.130, N:F.130, N:L.132, N:L.132, N:L.209, M:F.100 Hydrogen bonds: N:Y.80 Halogen bonds: M:D.96

14 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.8: 10 residues within 4Å: Chain A: R.40, L.41, I.46, Y.80 Chain G: L.66, F.67, S.70 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.1, WFP-ALO-PRO-YCP-ALA-MP8.1, WFP-ALO-PRO-YCP-ALA-MP8.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:R.40, A:L.41, A:L.41, G:L.66, G:L.66 OCA.9: 9 residues within 4Å: Chain A: L.66, S.70 Chain B: L.41, E.44, I.46, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.2, WFP-ALO-PRO-YCP-ALA-MP8.2, WFP-ALO-PRO-YCP-ALA-MP8.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.44, A:L.66 OCA.10: 8 residues within 4Å: Chain B: L.66, F.67, S.70 Chain C: L.41, E.44, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.3, WFP-ALO-PRO-YCP-ALA-MP8.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.66, B:F.67, C:L.41, C:E.44 OCA.11: 10 residues within 4Å: Chain C: L.66, F.67, S.70 Chain D: R.40, L.41, E.44, I.46, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.4, WFP-ALO-PRO-YCP-ALA-MP8.4 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:R.40, D:L.41, D:E.44, D:I.46, C:L.66 OCA.12: 9 residues within 4Å: Chain D: L.66, F.67, S.70 Chain E: L.41, I.46, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.5, WFP-ALO-PRO-YCP-ALA-MP8.5, WFP-ALO-PRO-YCP-ALA-MP8.5 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.67, E:L.41, E:I.46 OCA.13: 10 residues within 4Å: Chain E: L.66, F.67, S.70 Chain F: R.40, L.41, E.44, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.6, WFP-ALO-PRO-YCP-ALA-MP8.6, WFP-ALO-PRO-YCP-ALA-MP8.6 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:R.40, F:L.41, F:E.44, E:L.66 OCA.14: 7 residues within 4Å: Chain F: L.66, F.67, S.70 Chain G: L.41, E.44 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.7, WFP-ALO-PRO-YCP-ALA-MP8.7 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:L.41, G:L.41, G:E.44, F:L.66, F:L.66, F:F.67 Water bridges: F:E.69 OCA.22: 11 residues within 4Å: Chain H: R.40, L.41, E.44, I.46, Y.80 Chain N: L.66, F.67, S.70 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.15, WFP-ALO-PRO-YCP-ALA-MP8.15, WFP-ALO-PRO-YCP-ALA-MP8.15 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:R.40, H:L.41, H:E.44, H:I.46 OCA.23: 9 residues within 4Å: Chain H: L.66, F.67, S.70 Chain I: R.40, L.41, E.44, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.16, WFP-ALO-PRO-YCP-ALA-MP8.16 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:R.40, I:L.41, I:E.44 OCA.24: 10 residues within 4Å: Chain I: L.66, F.67, S.70 Chain J: R.40, L.41, I.46, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.17, WFP-ALO-PRO-YCP-ALA-MP8.17, WFP-ALO-PRO-YCP-ALA-MP8.17 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:R.40, J:L.41 OCA.25: 7 residues within 4Å: Chain J: L.66, S.70 Chain K: L.41, E.44, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.18, WFP-ALO-PRO-YCP-ALA-MP8.18 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: K:L.41, K:E.44, J:L.66 OCA.26: 8 residues within 4Å: Chain K: L.66, F.67, S.70 Chain L: L.41, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.19, WFP-ALO-PRO-YCP-ALA-MP8.19, WFP-ALO-PRO-YCP-ALA-MP8.19 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:F.67 OCA.27: 12 residues within 4Å: Chain L: L.66, F.67, E.69, S.70 Chain M: R.40, L.41, E.44, I.46, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.20, WFP-ALO-PRO-YCP-ALA-MP8.20, WFP-ALO-PRO-YCP-ALA-MP8.20 5 PLIP interactions: 4 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: M:R.40, M:L.41, M:E.44, M:I.46 Water bridges: L:E.69 OCA.28: 10 residues within 4Å: Chain M: L.66, F.67, S.70 Chain N: L.41, E.44, I.46, Y.80 Ligands: WFP-ALO-PRO-YCP-ALA-MP8.21, WFP-ALO-PRO-YCP-ALA-MP8.21, WFP-ALO-PRO-YCP-ALA-MP8.21 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:L.41, N:E.44, N:I.46, M:F.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun Biol (2019)

Release Date

2019-11-13

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
V

I
W

J
X

K
Y

L
Z

M
a

N
b

ATP-dependent Clp protease proteolytic subunit

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