SMTL ID : 6w9t.1

Crystal structure of Neisseria meningitidis ClpP protease complex with small molecule activator ACP1-06

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-14-mer

Ligands

14 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.80, A:I.83, A:P.85, H2O.2, H2O.2 K.2: 6 residues within 4Å: Chain B: M.80, N.81, I.83, P.85, D.86, V.87 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.80, B:P.85, H2O.6, H2O.7 K.3: 6 residues within 4Å: Chain C: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.80, C:I.83, C:P.85, H2O.9, H2O.11 K.4: 6 residues within 4Å: Chain D: M.80, N.81, I.83, P.85, D.86, V.87 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:M.80, D:I.83, D:P.85, H2O.13 K.5: 7 residues within 4Å: Chain E: M.80, N.81, I.83, K.84, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:M.80, E:I.83, E:P.85, H2O.16, H2O.18 K.7: 6 residues within 4Å: Chain F: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:M.80, F:I.83, F:P.85, H2O.20, H2O.21 K.8: 6 residues within 4Å: Chain G: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:M.80, G:I.83, H2O.24, H2O.25, H2O.27 K.9: 6 residues within 4Å: Chain H: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:M.80, H:I.83, H:P.85, H2O.29, H2O.30 K.10: 6 residues within 4Å: Chain I: M.80, N.81, I.83, P.85, D.86, V.87 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:M.80, I:P.85, H2O.33, H2O.34 K.11: 6 residues within 4Å: Chain J: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:M.80, J:I.83, J:P.85, H2O.36, H2O.38 K.12: 6 residues within 4Å: Chain K: M.80, N.81, I.83, P.85, D.86, V.87 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:M.80, K:I.83, K:P.85, H2O.40 K.13: 7 residues within 4Å: Chain L: M.80, N.81, I.83, K.84, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:M.80, L:I.83, L:P.85, H2O.43, H2O.45 K.15: 6 residues within 4Å: Chain M: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:M.80, M:I.83, M:P.85, H2O.47, H2O.48 K.16: 6 residues within 4Å: Chain N: M.80, N.81, I.83, P.85, D.86, V.87 5 PLIP interactions: 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:M.80, N:I.83, H2O.51, H2O.53, H2O.54

2 x KHS: N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide(Non-covalent)

KHS.6: 15 residues within 4Å: Chain E: L.48, E.51, S.52, P.55, F.82 Chain F: E.26, I.28, D.58, F.60, Y.62, S.88, K.110, F.112, L.191, R.194 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.60 Hydrogen bonds: F:Y.62, F:R.194, F:R.194 pi-Stacking: F:F.112 pi-Cation interactions: F:R.194 KHS.14: 15 residues within 4Å: Chain L: L.48, E.51, S.52, P.55, F.82 Chain M: E.26, I.28, D.58, F.60, Y.62, S.88, K.110, F.112, L.191, R.194 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:F.60 Hydrogen bonds: M:Y.62, M:R.194, M:R.194 pi-Stacking: M:F.112 pi-Cation interactions: M:R.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Binepal, G. et al., Development of Antibiotics That Dysregulate the Neisserial ClpP Protease. Acs Infect Dis. (2020)

Release Date

2020-12-09

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
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit