SMTL ID : 4u0g.1 (1 other biounit)

Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-7-7-mer

Ligands

7 x 39Y- WFP- THR- PRO- 3A0- ALA- PRO: ADEP-2B5Me(Non-covalent)

39Y-WFP-THR-PRO-3A0-ALA-PRO.1: 21 residues within 4Å: Chain A: L.49, V.50, E.52, S.53, T.80, Y.83, R.85 Chain B: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, L.192, R.195 Ligands: SO4.12 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:K.23, B:L.24, B:Y.63, B:V.91, B:L.93, B:L.115, B:L.192, A:L.49, A:L.49, A:V.50 Hydrogen bonds: B:Y.63, B:Y.63, B:Q.89, A:Y.83, A:R.85, A:R.85, A:R.85 pi-Stacking: A:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.2: 21 residues within 4Å: Chain A: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, T.190, L.192, R.195 Chain G: L.49, V.50, E.52, S.53, T.80, Y.83, R.85 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:K.23, A:L.24, A:I.29, A:Y.63, A:V.91, A:L.93, A:L.115, A:L.115, A:L.192, G:L.49 Hydrogen bonds: A:Y.63, A:Y.63, A:Q.89, G:Y.83, G:R.85, G:R.85 pi-Stacking: G:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.3: 23 residues within 4Å: Chain B: L.49, V.50, E.52, S.53, T.80, Y.83, R.85 Chain C: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, T.190, L.192, R.195 Ligands: SO4.18, SO4.19 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:L.49, B:V.50, C:K.23, C:L.24, C:Y.63, C:V.91, C:L.93, C:L.192 Hydrogen bonds: B:Y.83, B:R.85, B:R.85, C:Y.63, C:Y.63, C:Q.89 pi-Stacking: B:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.4: 17 residues within 4Å: Chain C: L.49, V.50, S.53, T.80, Y.83 Chain D: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, L.192 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:K.23, D:L.24, D:I.29, D:Y.63, D:V.91, D:L.93, D:L.192, C:L.49, C:L.49, C:V.50 Hydrogen bonds: D:Y.63, D:Y.63, D:Q.89, C:Y.83 pi-Stacking: C:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.5: 20 residues within 4Å: Chain D: L.49, V.50, E.52, S.53, T.80, Y.83, R.85 Chain E: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, L.192, R.195 16 PLIP interactions: 9 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:K.23, E:L.24, E:Y.63, E:V.91, E:L.93, E:L.192, D:L.49, D:L.49, D:V.50 Hydrogen bonds: E:Y.63, E:Y.63, E:Q.89, D:Y.83, D:R.85, D:R.85 pi-Stacking: D:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.6: 22 residues within 4Å: Chain E: L.49, V.50, E.52, S.53, T.80, Y.83, R.85 Chain F: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, T.190, L.192, R.195 Ligands: SO4.28 16 PLIP interactions: 6 interactions with chain E, 10 interactions with chain F Hydrophobic interactions: E:L.49, E:V.50, F:K.23, F:L.24, F:I.29, F:Y.63, F:V.91, F:L.93, F:L.192 Hydrogen bonds: E:Y.83, E:R.85, E:R.85, F:Y.63, F:Y.63, F:Q.89 pi-Stacking: E:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.7: 20 residues within 4Å: Chain F: L.49, V.50, S.53, T.80, Y.83, R.85 Chain G: K.23, L.24, E.27, I.29, T.61, Y.63, Q.89, V.91, L.93, M.113, L.115, T.190, L.192, R.195 18 PLIP interactions: 11 interactions with chain G, 7 interactions with chain F Hydrophobic interactions: G:K.23, G:L.24, G:Y.63, G:V.91, G:L.93, G:L.115, G:L.115, G:L.192, F:L.49, F:L.49, F:V.50 Hydrogen bonds: G:Y.63, G:Y.63, G:Q.89, F:Y.83, F:R.85, F:R.85 pi-Stacking: F:Y.83

14 x ZIL: N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine(Non-covalent)

ZIL.8: 19 residues within 4Å: Chain A: G.69, G.70, F.71, T.72, L.74, S.98, A.99, H.123, Q.124, P.125, S.126, L.127, Q.141, I.145, M.148, M.152 Chain B: R.119 Chain H: A.127, I.130 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.125, A:I.145 Hydrogen bonds: A:F.71, A:T.72, A:T.72, A:S.126 ZIL.11: 20 residues within 4Å: Chain B: G.69, G.70, F.71, T.72, L.74, S.98, A.99, V.102, H.123, Q.124, P.125, S.126, L.127, Q.141, I.145, M.148, M.152 Chain C: R.119 Chain I: A.127, I.130 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.71, B:P.125, B:I.145 Hydrogen bonds: B:F.71, B:T.72, B:T.72, B:S.126 ZIL.15: 19 residues within 4Å: Chain C: G.69, G.70, F.71, T.72, L.74, S.98, A.99, H.123, Q.124, P.125, S.126, L.127, Q.141, I.145, M.148, M.152 Chain D: R.119 Chain J: A.127, I.130 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.145 Hydrogen bonds: C:F.71, C:T.72, C:T.72, C:S.126 ZIL.21: 20 residues within 4Å: Chain D: G.69, G.70, F.71, T.72, L.74, S.98, A.99, V.102, H.123, Q.124, P.125, S.126, L.127, Q.141, I.145, M.148, M.152 Chain E: R.119 Chain K: A.127, I.130 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.71, D:P.125, D:I.145 Hydrogen bonds: D:F.71, D:T.72, D:T.72, D:S.126 ZIL.24: 20 residues within 4Å: Chain E: G.69, G.70, F.71, T.72, L.74, S.98, A.99, V.102, H.123, Q.124, P.125, S.126, L.127, Q.141, I.145, M.148, M.152 Chain F: R.119 Chain L: A.127, I.130 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.145 Hydrogen bonds: E:F.71, E:T.72, E:T.72, E:S.126 ZIL.30: 20 residues within 4Å: Chain F: G.69, G.70, F.71, T.72, L.74, S.98, A.99, H.123, Q.124, P.125, S.126, L.127, Q.141, E.144, I.145, M.148, M.152 Chain G: R.119 Chain M: A.127, I.130 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:P.125, F:I.145 Hydrogen bonds: F:F.71, F:T.72, F:T.72, F:S.126 ZIL.33: 20 residues within 4Å: Chain A: R.119 Chain G: G.69, G.70, F.71, T.72, L.74, S.98, A.99, V.102, H.123, Q.124, P.125, S.126, L.127, Q.141, I.145, M.148, M.152 Chain N: A.127, I.130 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain G Salt bridges: A:R.119 Hydrophobic interactions: G:P.125, G:I.145 Hydrogen bonds: G:F.71, G:T.72, G:T.72, G:S.126 ZIL.37: 20 residues within 4Å: Chain A: F.135 Chain H: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, Q.136, F.137, I.140, M.144, N.148 Chain N: R.113 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:I.65, H:F.96, H:F.137, H:I.140 Hydrogen bonds: H:G.63, H:I.65, H:L.120, H:L.120 ZIL.38: 21 residues within 4Å: Chain B: F.135 Chain H: R.113 Chain I: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, Q.136, F.137, I.140, M.144, F.145, N.148 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain B Hydrophobic interactions: I:I.65, I:F.96, I:F.137, I:I.140, B:F.135 Hydrogen bonds: I:G.63, I:I.65, I:L.120, I:L.120 ZIL.40: 21 residues within 4Å: Chain C: F.135 Chain I: R.113 Chain J: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, Q.136, F.137, I.140, M.144, F.145, N.148 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:F.96, J:F.137, J:I.140 Hydrogen bonds: J:G.63, J:I.65, J:L.120, J:L.120 ZIL.42: 21 residues within 4Å: Chain D: F.135 Chain J: R.113 Chain K: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, Q.136, F.137, I.140, M.144, F.145, N.148 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:I.65, K:F.96, K:F.137 Hydrogen bonds: K:G.63, K:I.65, K:L.120, K:L.120 ZIL.43: 20 residues within 4Å: Chain E: F.135 Chain K: R.113 Chain L: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, F.137, I.140, M.144, F.145, N.148 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain E Hydrophobic interactions: L:F.96, L:F.137, E:F.135 Hydrogen bonds: L:G.63, L:I.65, L:L.120, L:L.120 ZIL.44: 21 residues within 4Å: Chain F: F.135 Chain L: R.113 Chain M: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, Q.136, F.137, I.140, M.144, F.145, N.148 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:F.96, M:F.137, M:I.140 Hydrogen bonds: M:G.63, M:I.65, M:L.120, M:L.120 ZIL.46: 21 residues within 4Å: Chain G: F.135 Chain M: R.113 Chain N: G.63, S.64, I.65, S.66, S.92, M.93, F.96, H.117, Q.118, P.119, L.120, G.121, G.122, Q.136, F.137, I.140, M.144, F.145, N.148 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:P.119, N:F.137, N:I.140 Hydrogen bonds: N:G.63, N:I.65, N:L.120, N:L.120, N:G.122

17 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 2 residues within 4Å: Chain A: R.149, R.168 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: R.85 Chain B: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.1 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain C: R.149, R.168 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: R.58, D.59 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: R.85 Chain C: R.195, L.197 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.3 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.3 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain D: R.149, R.168 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain E: R.58, D.59 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain E: R.149, R.168 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain E: K.175 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain E: R.85 Chain F: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.6 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain F: R.149, R.168 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain G: R.58, D.59 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain G: R.149, R.168 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain I: R.158, R.167 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain J: R.158, R.167 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain M: D.49, K.52 Ligand excluded by PLIP

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 3 residues within 4Å: Chain A: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.12 DMS.13: 3 residues within 4Å: Chain B: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.12 DMS.14: 2 residues within 4Å: Chain B: R.149, R.168 No protein-ligand interaction detected (PLIP) DMS.20: 3 residues within 4Å: Chain C: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.12 DMS.23: 3 residues within 4Å: Chain D: S.11, S.12, F.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.12, D:S.12 DMS.29: 3 residues within 4Å: Chain E: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.12 DMS.32: 3 residues within 4Å: Chain F: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.12 DMS.36: 3 residues within 4Å: Chain G: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmitz, K.R. et al., Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-10-08

Peptides

ATP-dependent Clp protease proteolytic subunit 2: ABCDEFG
ATP-dependent Clp protease proteolytic subunit 1: HIJKLMN

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

ATP-dependent Clp protease proteolytic subunit 1

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