SMTL ID : 4u0g.2 (1 other biounit)

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

Coordinates

PDB Format

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: 20 residues within 4Å: Chain A: L.49, V.50, 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, T.190, L.192, R.195 16 PLIP interactions: 10 interactions with chain B, 6 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:V.50 Hydrogen bonds: B:Y.63, B:Y.63, B:Q.89, A:Y.83, A:R.85, A:R.85 pi-Stacking: A:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.2: 21 residues within 4Å: Chain B: L.49, V.50, 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: SO4.13 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:K.23, C:L.24, C:I.29, C:Y.63, C:V.91, C:L.93, C:L.115, C:L.192, B:L.49, B:V.50 Hydrogen bonds: C:Y.63, C:Y.63, C:Q.89, B:Y.83, B:R.85, B:R.85 pi-Stacking: B:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.3: 21 residues within 4Å: Chain C: L.49, V.50, S.53, T.80, Y.83, R.85 Chain D: 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: SO4.19 17 PLIP interactions: 10 interactions with chain D, 7 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, C:R.85, C:R.85 pi-Stacking: C:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.4: 21 residues within 4Å: Chain D: L.49, V.50, 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 Ligands: SO4.27, SO4.28 16 PLIP interactions: 10 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:K.23, E:L.24, E:Y.63, E:V.91, E:L.93, E:L.115, E:L.192, D:L.49 Hydrogen bonds: E:Y.63, E:Y.63, E:Q.89, D:Y.83, D:R.85, D:R.85, D:R.85 pi-Stacking: D:Y.83 39Y-WFP-THR-PRO-3A0-ALA-PRO.5: 20 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, L.192, R.195 16 PLIP interactions: 7 interactions with chain E, 9 interactions with chain F Hydrophobic interactions: E:L.49, E:V.50, F:K.23, F:L.24, F:Y.63, F:V.91, F:L.93, F:L.192 Hydrogen bonds: E:Y.83, E:R.85, 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.6: 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:I.29, G:Y.63, G:V.91, G:L.93, 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 39Y-WFP-THR-PRO-3A0-ALA-PRO.7: 23 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 Ligands: SO4.10, SO4.46 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain G Hydrophobic interactions: A:K.23, A:L.24, A:Y.63, A:V.91, A:L.93, A:L.192, G:L.49, G:L.49, G:V.50 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

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

ZIL.8: 20 residues within 4Å: Chain A: 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 B: R.119 Chain H: A.127, I.130 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.125, A:I.145 Hydrogen bonds: A:F.71, A:T.72, A:T.72, A:S.126 Salt bridges: B:R.119 ZIL.12: 19 residues within 4Å: Chain B: 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 C: R.119 Chain I: A.127, I.130 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.125, B:I.145 Hydrogen bonds: B:F.71, B:T.72, B:T.72, B:S.126 ZIL.17: 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, H.123, Q.124, P.125, S.126, L.127, Q.141, E.144, I.145, M.148, M.152 Chain E: R.119 Chain K: A.127, I.130 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.71, D:P.125, D:I.145, D:M.148 Hydrogen bonds: D:F.71, D:T.72, D:T.72, D:S.126 ZIL.26: 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 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.125, E:I.145 Hydrogen bonds: E:F.71, E:T.72, E:T.72, E:S.126 ZIL.32: 19 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, 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.35: 23 residues within 4Å: Chain A: Q.95, 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, E.144, I.145, M.148, M.152 Chain N: G.125, A.127, I.130 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:F.71, G:I.145 Hydrogen bonds: G:F.71, G:T.72, G:T.72, G:S.126 Salt bridges: A:R.119 ZIL.38: 21 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, F.145, N.148 Chain N: R.113 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:F.137, H:I.140 Hydrogen bonds: H:G.63, H:I.65, H:L.120, H:L.120 ZIL.39: 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 7 PLIP interactions: 7 interactions with chain I Hydrophobic interactions: I:F.96, I:P.119, I:F.137 Hydrogen bonds: I:G.63, I:I.65, I:L.120, I:L.120 ZIL.41: 20 residues within 4Å: Chain C: F.135 Chain I: R.113 Chain J: G.63, S.64, I.65, 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 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: 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.137, K:I.140 Hydrogen bonds: K:G.63, K:I.65, K:L.120, K:L.120 ZIL.43: 21 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, Q.136, F.137, I.140, M.144, F.145, N.148 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain E Hydrophobic interactions: L:P.119, L:I.140, E:F.135 Hydrogen bonds: L:G.63, L:I.65, L:L.120, L:L.120, L:G.122 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: 6 interactions with chain M, 1 interactions with chain F Hydrophobic interactions: M:P.119, M:I.140, F:F.135 Hydrogen bonds: M:G.63, M:I.65, M:L.120, M:L.120 ZIL.45: 20 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, N.148 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:I.65, N:F.137 Hydrogen bonds: N:G.63, N:I.65, N:L.120, N:L.120

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

SO4.9: 2 residues within 4Å: Chain A: R.149, R.168 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: R.195 Chain G: R.85 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.7 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: R.85 Chain C: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.2 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.149, R.168 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: R.58, D.59 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: R.149, R.168 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: R.85 Chain D: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.3 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain D: R.58, D.59 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain D: K.175 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: R.149, R.168 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain D: R.85 Chain E: R.195, L.197 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.4 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain E: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.4 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain E: R.58, D.59 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain E: R.149, R.168 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain F: R.149, R.168 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain G: R.149, R.168 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain I: R.158, R.167 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain A: R.195 Ligands: 39Y-WFP-THR-PRO-3A0-ALA-PRO.7 Ligand excluded by PLIP

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

DMS.11: 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.16: 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.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.25: 3 residues within 4Å: Chain D: S.11, S.12, F.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.12 DMS.31: 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.34: 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.37: 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
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 2

ATP-dependent Clp protease proteolytic subunit 1

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