SMTL ID : 7mk5.2 (1 other biounit)

Crystal structure of Escherichia coli ClpP covalently inhibited by clipibicyclene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-14-mer

Ligands

25 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 14 residues within 4Å: Chain A: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.3 Ligand excluded by PLIP MPD.2: 12 residues within 4Å: Chain A: I.70, M.74, E.141, K.144, V.145, R.148, M.149 Chain B: N.116, S.117, R.118, S.175, A.176 Ligand excluded by PLIP MPD.4: 14 residues within 4Å: Chain B: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.6 Ligand excluded by PLIP MPD.5: 12 residues within 4Å: Chain B: I.70, M.74, E.141, K.144, V.145, R.148, M.149 Chain C: N.116, S.117, R.118, S.175, A.176 Ligand excluded by PLIP MPD.8: 13 residues within 4Å: Chain C: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.10 Ligand excluded by PLIP MPD.9: 9 residues within 4Å: Chain B: L.48, E.51, A.52, F.82 Chain C: L.23, E.26, V.28, Y.60, Y.62 Ligand excluded by PLIP MPD.11: 12 residues within 4Å: Chain C: I.70, T.71, M.74, E.141, K.144, V.145, R.148 Chain D: N.116, S.117, R.118, S.175, A.176 Ligand excluded by PLIP MPD.12: 14 residues within 4Å: Chain D: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.14 Ligand excluded by PLIP MPD.15: 10 residues within 4Å: Chain D: M.74, E.141, K.144, V.145, R.148, M.149 Chain E: N.116, S.117, R.118, S.175 Ligand excluded by PLIP MPD.16: 14 residues within 4Å: Chain E: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.17 Ligand excluded by PLIP MPD.18: 13 residues within 4Å: Chain E: I.70, T.71, M.74, E.141, K.144, V.145, R.148, M.149 Chain F: N.116, S.117, R.118, S.175, A.176 Ligand excluded by PLIP MPD.19: 13 residues within 4Å: Chain F: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.20 Ligand excluded by PLIP MPD.21: 13 residues within 4Å: Chain G: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.22 Ligand excluded by PLIP MPD.23: 14 residues within 4Å: Chain H: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.24 Ligand excluded by PLIP MPD.25: 11 residues within 4Å: Chain H: N.116, S.117, R.118, S.175, A.176 Chain I: M.74, E.141, K.144, V.145, R.148, M.149 Ligand excluded by PLIP MPD.26: 13 residues within 4Å: Chain I: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.27 Ligand excluded by PLIP MPD.28: 12 residues within 4Å: Chain J: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153 Ligands: ZGV.30 Ligand excluded by PLIP MPD.31: 13 residues within 4Å: Chain K: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.32 Ligand excluded by PLIP MPD.33: 11 residues within 4Å: Chain K: N.116, S.117, R.118, S.175 Chain L: I.70, M.74, E.141, K.144, V.145, R.148, M.149 Ligand excluded by PLIP MPD.34: 14 residues within 4Å: Chain L: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.37 Ligand excluded by PLIP MPD.35: 14 residues within 4Å: Chain L: N.116, S.117, R.118, F.173, L.174, S.175 Chain M: I.70, T.71, M.74, E.141, K.144, V.145, R.148, M.149 Ligand excluded by PLIP MPD.38: 14 residues within 4Å: Chain M: I.70, S.97, M.98, A.100, F.101, M.120, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.39 Ligand excluded by PLIP MPD.40: 10 residues within 4Å: Chain M: N.116, S.117, R.118, S.175 Chain N: M.74, E.141, K.144, V.145, R.148, M.149 Ligand excluded by PLIP MPD.41: 13 residues within 4Å: Chain N: I.70, S.97, M.98, A.100, F.101, I.121, H.122, Q.123, P.124, M.149, M.153, T.168 Ligands: ZGV.43 Ligand excluded by PLIP MPD.42: 15 residues within 4Å: Chain H: I.70, T.71, M.74, E.141, K.144, V.145, R.148, M.149 Chain N: G.93, N.116, S.117, R.118, L.174, S.175, A.176 Ligand excluded by PLIP

14 x ZGV: 4-[(1E)-3-{[(2E,4E,6E,8S)-8-hydroxy-4-methyldeca-2,4,6-trienoyl]amino}-3-oxoprop-1-en-1-yl]azete-1(2H)-carboxylic acid(Covalent)

ZGV.3: 18 residues within 4Å: Chain A: Q.34, P.66, G.67, G.68, I.70, Q.94, A.96, S.97, M.98, R.118, M.120, H.122, Q.123, P.124, L.125, F.173 Chain G: H.138 Ligands: MPD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.66, A:I.70, A:L.125, A:F.173 Hydrogen bonds: A:G.68, A:M.98 ZGV.6: 10 residues within 4Å: Chain B: Q.34, G.67, G.68, I.70, S.97, M.98, H.122, P.124, L.125 Ligands: MPD.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.70 Hydrogen bonds: B:H.122 ZGV.10: 12 residues within 4Å: Chain C: Q.34, P.66, G.67, G.68, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.34, C:G.68, C:M.98 ZGV.14: 9 residues within 4Å: Chain D: G.67, G.68, I.70, S.97, M.98, H.122, P.124, L.125 Ligands: MPD.12 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.125 Hydrogen bonds: D:G.68, D:M.98 ZGV.17: 13 residues within 4Å: Chain E: Q.34, P.66, G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.16 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.70, E:L.125 Hydrogen bonds: E:Q.34, E:G.68, E:M.98 ZGV.20: 12 residues within 4Å: Chain F: Q.34, P.66, G.67, G.68, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.19 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:P.66, F:L.125 Hydrogen bonds: F:G.68, F:M.98 ZGV.22: 13 residues within 4Å: Chain G: Q.34, P.66, G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.21 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.68, G:M.98 ZGV.24: 11 residues within 4Å: Chain H: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.23 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.68 ZGV.27: 12 residues within 4Å: Chain I: Q.34, P.66, G.67, G.68, I.70, S.97, M.98, H.122, P.124, L.125 Chain J: V.69 Ligands: MPD.26 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:L.125 Hydrogen bonds: I:G.68 ZGV.30: 11 residues within 4Å: Chain J: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.28 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:I.70, J:L.125 Hydrogen bonds: J:G.68 ZGV.32: 13 residues within 4Å: Chain K: Q.34, P.66, G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.31 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:P.66, K:I.70 ZGV.37: 11 residues within 4Å: Chain L: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.34 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:I.70, L:L.125 Hydrogen bonds: L:G.68, L:M.98 ZGV.39: 11 residues within 4Å: Chain M: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.38 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:I.70, M:L.125 Hydrogen bonds: M:G.68, M:M.98 ZGV.43: 12 residues within 4Å: Chain N: Q.34, G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125 Ligands: MPD.41 3 PLIP interactions: 3 interactions with chain N Hydrophobic interactions: N:I.70 Hydrogen bonds: N:Q.34, N:G.68

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 8 residues within 4Å: Chain B: E.136, A.139, R.140, L.143 Chain I: E.136, A.139, R.140, L.143 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.139 ACT.13: 8 residues within 4Å: Chain D: E.136, A.139, R.140, L.143 Chain K: E.136, A.139, R.140, L.143 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain D Hydrogen bonds: K:E.136 Hydrophobic interactions: D:R.140 ACT.29: 4 residues within 4Å: Chain C: E.136 Chain J: E.136, A.139, R.140 No protein-ligand interaction detected (PLIP) ACT.36: 5 residues within 4Å: Chain E: E.136, A.139, R.140 Chain L: E.136, R.140 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.136 Salt bridges: L:R.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Culp, E.J. et al., ClpP inhibitors are produced by a widespread family of bacterial gene clusters. Nat Microbiol (2022)

Release Date

2022-02-02

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

E
S

F
T

G
U

H
V

I
W

J
X

K
Y

L
Z

M
a

N
b

ATP-dependent Clp protease proteolytic subunit

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