SMTL ID : 2fzs.1

Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

14 x CMQ: N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE(Covalent)

CMQ.1: 14 residues within 4Å: Chain A: G.67, G.68, V.69, I.70, S.97, M.98, H.122, P.124, L.125, E.141, I.142, V.145, M.149 Ligands: GOL.6 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.70, A:I.70, A:M.98, A:P.124, A:L.125, A:E.141, A:I.142, A:I.142, A:V.145, A:M.149 Hydrogen bonds: A:G.68, A:G.68, A:G.68, A:I.70, A:M.98, A:L.125, A:L.125, A:M.149 Water bridges: A:T.71, A:N.150 CMQ.4: 15 residues within 4Å: Chain B: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125, E.141, I.142, M.149, N.150 Ligands: GOL.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.69, B:I.70, B:I.70, B:M.98, B:P.124, B:L.125, B:E.141, B:I.142, B:I.142 Hydrogen bonds: B:G.68, B:G.68, B:G.68, B:I.70, B:M.98, B:L.125, B:L.125 Water bridges: B:T.71, B:M.149, B:N.150, B:N.150 CMQ.8: 14 residues within 4Å: Chain C: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125, E.141, I.142, M.149 Ligands: GOL.11 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.69, C:I.70, C:M.98, C:P.124, C:L.125, C:E.141, C:I.142, C:I.142, C:I.142 Hydrogen bonds: C:G.68, C:G.68, C:G.68, C:I.70, C:M.98, C:L.125, C:L.125, C:M.149 Water bridges: C:T.71, C:N.150 CMQ.12: 12 residues within 4Å: Chain D: G.67, G.68, V.69, I.70, S.97, M.98, H.122, P.124, L.125, E.141, I.142, M.149 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.69, D:I.70, D:I.70, D:P.124, D:E.141, D:I.142, D:I.142, D:I.142 Hydrogen bonds: D:G.68, D:G.68, D:G.68, D:I.70, D:M.98, D:L.125, D:L.125, D:M.149 Water bridges: D:T.71 CMQ.14: 17 residues within 4Å: Chain E: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125, E.141, I.142, V.145, M.149, N.150, M.153 Chain F: R.118 24 PLIP interactions: 24 interactions with chain E Hydrophobic interactions: E:V.69, E:I.70, E:I.70, E:M.98, E:P.124, E:L.125, E:E.141, E:I.142, E:I.142, E:I.142, E:V.145 Hydrogen bonds: E:G.68, E:G.68, E:G.68, E:I.70, E:M.98, E:L.125, E:L.125 Water bridges: E:T.71, E:H.122, E:H.122, E:M.149, E:N.150, E:N.150 CMQ.16: 15 residues within 4Å: Chain F: G.67, G.68, V.69, I.70, S.97, M.98, F.101, H.122, P.124, L.125, E.141, I.142, M.149, N.150 Ligands: GOL.21 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:V.69, F:I.70, F:I.70, F:F.101, F:P.124, F:L.125, F:E.141, F:I.142 Hydrogen bonds: F:G.68, F:G.68, F:G.68, F:I.70, F:M.98, F:L.125, F:L.125 Water bridges: F:T.71, F:N.150, F:N.150 CMQ.19: 14 residues within 4Å: Chain A: R.118 Chain G: Q.34, G.67, G.68, V.69, I.70, S.97, M.98, H.122, P.124, L.125, I.142, M.149, N.150 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:V.69, G:I.70, G:I.70, G:M.98, G:L.125, G:I.142, G:I.142 Hydrogen bonds: G:G.68, G:G.68, G:G.68, G:I.70, G:M.98, G:L.125, G:L.125 Water bridges: G:T.71, G:N.150 CMQ.22: 15 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, E.141, I.142, M.149, N.150 Ligands: GOL.40 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:V.69, H:I.70, H:I.70, H:M.98, H:P.124, H:L.125, H:E.141, H:I.142, H:I.142, H:I.142 Hydrogen bonds: H:G.68, H:G.68, H:G.68, H:I.70, H:M.98, H:L.125, H:L.125 Water bridges: H:T.71, H:N.150 CMQ.25: 15 residues within 4Å: Chain I: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125, E.141, I.142, M.149, N.150 Ligands: GOL.24 18 PLIP interactions: 18 interactions with chain I Hydrophobic interactions: I:V.69, I:I.70, I:I.70, I:P.124, I:L.125, I:E.141, I:I.142, I:I.142, I:I.142 Hydrogen bonds: I:G.68, I:G.68, I:G.68, I:I.70, I:M.98, I:L.125, I:L.125 Water bridges: I:T.71, I:N.150 CMQ.27: 14 residues within 4Å: Chain J: G.67, G.68, V.69, I.70, S.97, M.98, H.122, P.124, L.125, E.141, I.142, V.145, M.149, N.150 18 PLIP interactions: 18 interactions with chain J Hydrophobic interactions: J:V.69, J:I.70, J:I.70, J:M.98, J:P.124, J:E.141, J:I.142, J:I.142, J:V.145, J:M.149 Hydrogen bonds: J:G.68, J:G.68, J:I.70, J:M.98, J:L.125, J:L.125 Water bridges: J:T.71, J:N.150 CMQ.29: 14 residues within 4Å: Chain K: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125, E.141, I.142, M.149, N.150 20 PLIP interactions: 20 interactions with chain K Hydrophobic interactions: K:V.69, K:I.70, K:I.70, K:M.98, K:P.124, K:L.125, K:E.141, K:I.142, K:I.142 Hydrogen bonds: K:G.68, K:G.68, K:G.68, K:I.70, K:M.98, K:L.125, K:L.125 Water bridges: K:T.71, K:M.149, K:N.150, K:N.150 CMQ.33: 14 residues within 4Å: Chain L: G.67, G.68, V.69, I.70, S.97, M.98, H.122, P.124, L.125, E.141, I.142, M.149, N.150 Ligands: GOL.32 18 PLIP interactions: 18 interactions with chain L Hydrophobic interactions: L:I.70, L:I.70, L:M.98, L:P.124, L:L.125, L:E.141, L:I.142, L:M.149 Hydrogen bonds: L:G.68, L:G.68, L:G.68, L:I.70, L:M.98, L:L.125, L:L.125, L:M.149 Water bridges: L:T.71, L:N.150 CMQ.36: 16 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, E.141, I.142, V.145, M.149, N.150 Ligands: GOL.35 20 PLIP interactions: 20 interactions with chain M Hydrophobic interactions: M:V.69, M:I.70, M:I.70, M:M.98, M:P.124, M:L.125, M:E.141, M:I.142, M:I.142, M:V.145 Hydrogen bonds: M:G.68, M:G.68, M:G.68, M:I.70, M:M.98, M:L.125, M:L.125, M:M.149 Water bridges: M:T.71, M:N.150 CMQ.38: 15 residues within 4Å: Chain N: G.67, G.68, V.69, I.70, S.97, M.98, H.122, Q.123, P.124, L.125, E.141, I.142, V.145, M.149, M.153 20 PLIP interactions: 20 interactions with chain N Hydrophobic interactions: N:V.69, N:I.70, N:I.70, N:M.98, N:P.124, N:L.125, N:E.141, N:I.142, N:V.145, N:M.149 Hydrogen bonds: N:G.68, N:G.68, N:G.68, N:I.70, N:M.98, N:L.125, N:L.125, N:M.149 Water bridges: N:T.71, N:N.150

15 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: Y.60, Y.62, I.90, F.112, L.189, R.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.192 Water bridges: A:R.192, A:R.192, A:R.192 PGE.5: 6 residues within 4Å: Chain B: E.26, Y.60, Y.62, I.90, R.192, N.193 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.26, B:E.26, B:R.192, B:R.192 PGE.9: 5 residues within 4Å: Chain C: Y.60, Y.62, I.90, L.189, R.192 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.62, C:R.192 Water bridges: C:R.192, C:R.192 PGE.13: 7 residues within 4Å: Chain D: V.28, Y.60, Y.62, I.90, F.112, L.189, R.192 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.62, D:R.192 Water bridges: D:R.192 PGE.15: 4 residues within 4Å: Chain E: Y.60, Y.62, L.189, R.192 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.62, E:R.192 Water bridges: E:S.88, E:R.192, E:R.192 PGE.17: 5 residues within 4Å: Chain F: Y.60, Y.62, F.112, L.189, R.192 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.60, F:Y.62, F:R.192, F:R.192 PGE.20: 4 residues within 4Å: Chain G: V.28, Y.60, Y.62, R.192 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:R.192 Water bridges: G:Y.60, G:R.192 PGE.23: 8 residues within 4Å: Chain H: V.28, Y.60, Y.62, I.90, F.112, L.189, R.192 Chain I: F.82 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:Y.62, H:R.192, H:R.192 PGE.26: 6 residues within 4Å: Chain I: Y.60, Y.62, I.90, F.112, L.189, R.192 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.192 Water bridges: I:S.88 PGE.28: 8 residues within 4Å: Chain J: V.28, Y.60, Y.62, F.112, L.189, R.192 Chain K: L.48, F.82 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:R.192, J:R.192 Water bridges: J:S.88, J:N.193, J:N.193 PGE.30: 6 residues within 4Å: Chain K: Y.60, Y.62, I.90, L.189, R.192 Chain L: L.48 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.192, K:R.192 PGE.31: 6 residues within 4Å: Chain K: T.157, G.158, Q.159, E.181, Y.182, G.183 1 PLIP interactions: 1 interactions with chain K Water bridges: K:S.160 PGE.34: 6 residues within 4Å: Chain L: V.28, Y.60, Y.62, F.112, L.189, R.192 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:R.192 Water bridges: L:R.192, L:R.192 PGE.37: 7 residues within 4Å: Chain M: V.28, Y.60, Y.62, I.90, F.112, L.189, R.192 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.192 Water bridges: M:R.192 PGE.39: 7 residues within 4Å: Chain H: F.82 Chain N: V.28, Y.60, Y.62, F.112, L.189, R.192 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:Y.62, N:R.192, N:R.192

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: R.118, F.173, L.174, S.175 Chain G: E.141, K.144, V.145, R.148 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain A Water bridges: G:E.141, G:K.144, G:K.144, G:R.148, A:F.173 GOL.6: 6 residues within 4Å: Chain A: T.71, E.141 Chain B: Q.94, R.118, F.173 Ligands: CMQ.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.94, B:Q.94, B:Q.94 Hydrogen bonds: A:E.141 GOL.7: 5 residues within 4Å: Chain B: T.157, Q.159, E.181, Y.182, G.183 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.180 GOL.10: 7 residues within 4Å: Chain B: T.71, E.141 Chain C: Q.94, R.118, M.120, F.173 Ligands: CMQ.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.141 GOL.11: 6 residues within 4Å: Chain C: T.71, E.141 Chain D: Q.94, R.118, F.173 Ligands: CMQ.8 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:T.71, D:Q.94 GOL.18: 7 residues within 4Å: Chain E: E.141, K.144, V.145 Chain F: R.118, F.173, L.174, S.175 3 PLIP interactions: 3 interactions with chain E Water bridges: E:E.141, E:K.144, E:K.144 GOL.21: 7 residues within 4Å: Chain F: T.71, E.141, V.145 Chain G: Q.94, R.118, F.173 Ligands: CMQ.16 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Water bridges: G:Q.94 Hydrogen bonds: F:E.141 GOL.24: 6 residues within 4Å: Chain H: Q.94, R.118, F.173 Chain I: E.141, V.145 Ligands: CMQ.25 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:Q.94, H:R.118 Water bridges: H:Q.94, I:H.138 GOL.32: 9 residues within 4Å: Chain K: Q.94, A.96, R.118, M.120, F.173 Chain L: T.71, E.141, V.145 Ligands: CMQ.33 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.141, L:E.141 GOL.35: 6 residues within 4Å: Chain L: Q.94, R.118, F.173 Chain M: T.71, E.141 Ligands: CMQ.36 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:E.141, M:E.141 GOL.40: 8 residues within 4Å: Chain H: T.71, E.141, V.145 Chain N: Q.94, R.118, M.120, F.173 Ligands: CMQ.22 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.141, H:E.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szyk, A. et al., Crystal structure at 1.9A of E. coli ClpP with a peptide covalently bound at the active site. J.Struct.Biol. (2006)

Release Date

2006-05-23

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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