SMTL ID : 8dla.1

ClpP2 from Chlamydia trachomatis bound by MAS1-12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-14-mer

Ligands

6 x UER: 1-{4-[(4-chlorophenyl)methyl]piperazin-1-yl}-2-methyl-2-[5-(trifluoromethyl)pyridine-2-sulfonyl]propan-1-one(Non-covalent)

UER.1: 5 residues within 4Å: Chain A: Q.61, A.193, K.194, E.195, T.196 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.193 UER.2: 14 residues within 4Å: Chain A: L.49, M.52, F.83 Chain C: K.26, D.27, R.28, I.29, Q.61, F.63, Y.91, I.93, L.115, A.193, K.199 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:D.27, C:A.193, A:F.83, A:F.83 pi-Stacking: C:F.63, C:Y.91 UER.3: 9 residues within 4Å: Chain B: I.29, K.58, D.59, Q.61, Y.91, K.197, D.198, S.200 Chain L: M.52 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.197 pi-Cation interactions: B:K.197 UER.7: 14 residues within 4Å: Chain D: D.27, K.58, Q.61, F.63, Y.91, I.93, L.115, A.193, T.196, K.199, S.200, I.201 Chain G: M.52, F.83 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:K.58, D:Q.61, D:F.63, D:F.63, D:Y.91, D:I.201, G:F.83 UER.12: 12 residues within 4Å: Chain G: Q.61, F.63, Y.91, I.93, K.111, L.115, I.190, A.193, K.194 Chain I: L.49, M.52, F.83 5 PLIP interactions: 3 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: I:L.49, I:F.83, I:F.83, G:F.63, G:F.63 UER.16: 9 residues within 4Å: Chain D: M.52, S.53, F.83 Chain M: D.27, Q.61, F.63, Y.91, K.197, I.201 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:D.27, M:K.197, M:I.201 Hydrogen bonds: M:Q.61 pi-Cation interactions: M:K.197

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

NA.4: 7 residues within 4Å: Chain B: H.123, P.125, S.126, D.172 Chain M: H.123, P.125, D.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.126, B:D.172 NA.8: 4 residues within 4Å: Chain D: H.123, D.172 Chain N: H.123, D.172 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain D Hydrogen bonds: N:H.123, N:D.172, D:D.172 Water bridges: N:S.126 NA.9: 3 residues within 4Å: Chain E: G.176, E.178, E.179 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.176, E:E.178, E:E.179, E:E.179, E:E.179 NA.10: 4 residues within 4Å: Chain F: G.176, A.177, E.178, E.179 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.178, F:E.179 Water bridges: F:A.177 NA.13: 7 residues within 4Å: Chain G: H.123, P.125, S.126, D.172 Chain K: H.123, D.172 Chain N: Q.139 4 PLIP interactions: 1 interactions with chain N, 2 interactions with chain G, 1 interactions with chain K Hydrogen bonds: N:Q.139, G:S.126, G:D.172, K:D.172 NA.14: 4 residues within 4Å: Chain C: Q.139 Chain H: H.123, Q.124, S.169 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:Q.124, H:Q.124, C:Q.139 NA.15: 7 residues within 4Å: Chain H: H.123, D.172 Chain L: H.123, P.125, S.126, G.127, D.172 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:S.126, L:G.127, L:D.172 NA.18: 3 residues within 4Å: Chain N: G.176, A.177, E.178 4 PLIP interactions: 4 interactions with chain N Hydrogen bonds: N:A.177, N:E.178 Water bridges: N:R.119, N:G.176

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain B: S.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.133 GOL.6: 3 residues within 4Å: Chain C: Y.21, M.31, Q.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.21, C:Q.47 GOL.11: 9 residues within 4Å: Chain G: G.94, H.117, S.118, R.119 Chain I: T.72, L.75, A.76, D.79, L.146 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I Hydrogen bonds: G:G.94, G:H.117, I:D.79, I:D.79 GOL.17: 8 residues within 4Å: Chain B: T.72, L.138, E.142, L.146 Chain N: G.94, Q.95, R.119, F.174 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain B Hydrogen bonds: N:G.94, B:E.142, B:E.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Azadmanesh, J. et al., The structure of caseinolytic protease subunit ClpP2 reveals a functional model of the caseinolytic protease system from Chlamydia trachomatis. J.Biol.Chem. (2023)

Release Date

2023-08-09

Peptides

ATP-dependent Clp protease proteolytic subunit 2: 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 2

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