SMTL ID : 9if4.1

Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-7-1-mer

Ligands

7 x S0R- LEU: activator Bz-Leu-Leu(Non-covalent)

S0R-LEU.1: 17 residues within 4Å: Chain G: G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, Q.139, I.143, M.146, M.150 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:F.69, G:L.72, G:P.123, G:L.125, G:I.143 Hydrogen bonds: G:G.67, G:F.69, G:S.124, G:S.124, G:S.126, G:S.126 S0R-LEU.2: 18 residues within 4Å: Chain H: Q.33, G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, E.142, I.143, M.146, M.150 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:F.69, H:L.72, H:A.97, H:L.125, H:I.143 Hydrogen bonds: H:G.67, H:S.124, H:S.124, H:S.126 S0R-LEU.3: 17 residues within 4Å: Chain I: Q.33, G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, I.143, M.146, M.150 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:F.69, I:F.69, I:L.72, I:A.97, I:P.123 Hydrogen bonds: I:G.67, I:F.69, I:S.124, I:S.124, I:S.124, I:S.126, I:S.126 S0R-LEU.4: 19 residues within 4Å: Chain J: Q.33, G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, I.143, M.146, M.150 Chain P: A.120, I.123 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:F.69, J:L.72, J:A.97, J:I.143, J:I.143 Hydrogen bonds: J:G.67, J:F.69, J:S.124, J:S.124 S0R-LEU.5: 19 residues within 4Å: Chain K: G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, I.129, I.143, M.146, M.150 Chain R: A.120, I.123 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:F.69, K:L.72, K:A.97, K:L.125, K:I.143 Hydrogen bonds: K:G.67, K:F.69, K:S.124, K:S.124 S0R-LEU.6: 16 residues within 4Å: Chain L: G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, I.143, M.146, M.150 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:F.69, L:F.69, L:P.123 Hydrogen bonds: L:G.67, L:S.124, L:S.124, L:S.124, L:S.126 S0R-LEU.7: 16 residues within 4Å: Chain T: G.67, G.68, F.69, L.72, S.96, A.97, V.100, H.121, Q.122, P.123, S.124, L.125, S.126, I.143, M.146, M.150 10 PLIP interactions: 10 interactions with chain T Hydrophobic interactions: T:F.69, T:F.69, T:L.72, T:P.123 Hydrogen bonds: T:G.67, T:F.69, T:S.124, T:S.124, T:S.126, T:S.126

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.8: 19 residues within 4Å: Chain A: P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, P.183, H.187, I.191, L.195, P.229, D.230, I.233 Chain F: R.173 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:I.24, A:I.24, A:R.26, A:G.52, A:G.54, A:K.55, A:T.56, A:T.56, A:T.56, A:A.57, F:R.173 Salt bridges: A:K.55, F:R.173 ADP.9: 14 residues within 4Å: Chain A: I.351, I.352, Q.354, G.391, K.392, E.394, M.563, L.566, M.567, F.597, R.604, P.605, L.606, R.607 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.352, A:Q.354, A:G.391, A:R.604, A:L.606, A:R.607, A:R.607 ADP.18: 20 residues within 4Å: Chain E: R.173 Chain F: P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, E.121, H.187, I.191, L.195, Y.199, P.229, D.230, I.233 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:I.24, F:I.24, F:R.26, F:G.52, F:V.53, F:G.54, F:K.55, F:T.56, F:T.56, F:A.57, F:E.121 Salt bridges: F:K.55 ADP.19: 11 residues within 4Å: Chain E: N.544 Chain F: G.389, V.390, G.391, K.392, T.393, E.394, M.563, M.567, A.603, R.604 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:N.544, F:G.391, F:K.392, F:K.392, F:T.393, F:R.604, F:R.604

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.10: 23 residues within 4Å: Chain A: R.147, A.170, R.173, R.174 Chain B: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, T.157, H.187, I.191, L.195, P.229, D.230, I.233 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:I.24, B:I.24, B:R.26, B:G.52, B:V.53, B:G.54, B:K.55, B:T.56, B:T.56, B:T.56, B:A.57 Salt bridges: B:K.55, B:K.55, A:R.147, A:R.173, A:R.173, A:R.173, A:R.174 ATP.11: 21 residues within 4Å: Chain B: R.350, I.351, I.352, Q.354, S.388, G.389, V.390, G.391, K.392, T.393, E.394, E.459, N.500, L.555, M.563, L.566, M.567, R.570, A.603, R.604, R.607 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:I.352, B:I.352, B:G.389, B:V.390, B:G.391, B:K.392, B:T.393, B:T.393, B:T.393, B:E.394, B:E.459, B:E.459, B:N.500 Salt bridges: B:K.392, B:K.392, B:R.604, B:R.604, B:R.604 ATP.12: 24 residues within 4Å: Chain B: R.147, A.170, R.173, R.174 Chain C: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, T.157, H.187, I.191, L.195, Y.199, P.229, D.230, I.233 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:I.24, C:I.24, C:R.26, C:G.52, C:V.53, C:G.54, C:K.55, C:T.56, C:T.56, C:A.57, B:R.147 Salt bridges: C:K.55, C:K.55, B:R.173, B:R.173, B:R.173, B:R.174 ATP.13: 23 residues within 4Å: Chain B: E.476, E.541, R.545 Chain C: R.350, I.351, I.352, Q.354, S.388, G.389, V.390, G.391, K.392, T.393, E.394, E.459, N.500, L.555, M.563, L.566, M.567, A.603, R.604, R.607 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.352, C:G.389, C:V.390, C:V.390, C:G.391, C:K.392, C:T.393, C:T.393, C:E.394, C:E.459, C:E.459 Salt bridges: C:K.392, C:K.392, C:R.604, C:R.604, C:R.604, B:R.545 ATP.14: 24 residues within 4Å: Chain C: T.41, A.170, R.173, R.174 Chain D: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, E.121, T.157, I.191, L.195, Y.199, P.229, D.230, I.233 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:D.21, D:I.24, D:G.52, D:G.54, D:K.55, D:T.56, D:T.56, D:A.57, D:E.121, D:T.157 Salt bridges: D:K.55, D:K.55, C:R.173, C:R.173, C:R.173, C:R.174 ATP.15: 22 residues within 4Å: Chain C: E.476, E.541, R.545 Chain D: R.350, I.351, I.352, Q.354, S.388, G.389, V.390, G.391, K.392, T.393, E.394, N.500, L.555, M.563, L.566, M.567, A.603, R.604, R.607 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.352, D:I.352, D:G.389, D:V.390, D:G.391, D:K.392, D:T.393, D:E.394, D:R.607 Salt bridges: D:K.392, D:K.392, D:R.604, D:R.604, D:R.604, C:R.545 ATP.16: 21 residues within 4Å: Chain D: R.147, A.170, R.173, R.174 Chain E: D.21, P.22, V.23, I.24, R.26, P.51, G.52, V.53, G.54, K.55, T.56, A.57, H.187, I.191, L.195, P.229, I.233 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:I.24, E:I.24, E:R.26, E:G.52, E:G.54, E:K.55, E:T.56, E:T.56, E:A.57, D:A.170 Salt bridges: E:K.55, E:K.55, D:R.173, D:R.173, D:R.173, D:R.174 ATP.17: 23 residues within 4Å: Chain D: E.476, E.541, R.545 Chain E: R.350, I.351, I.352, Q.354, S.388, G.389, V.390, G.391, K.392, T.393, E.394, E.459, N.500, L.555, M.563, L.566, M.567, A.603, R.604, R.607 19 PLIP interactions: 17 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:I.352, E:G.389, E:V.390, E:V.390, E:G.391, E:K.392, E:T.393, E:T.393, E:T.393, E:E.394, E:E.459, E:R.607, D:E.476 Salt bridges: E:K.392, E:K.392, E:R.604, E:R.604, E:R.604, D:R.545

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weinhaeupl, K. et al., Structure of the Mycobacterium Tuberculosis ClpC1P1P2 complex bound to the activator Bz-Leu-Leu. To Be Published

Release Date

2025-08-27

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpC1: ABCDEF
ATP-dependent Clp protease proteolytic subunit 2: GHIJKLT
ATP-dependent Clp protease proteolytic subunit 1: MNOPQRS
Unknown peptide: U

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
L

L
M

T
K

M
N

N
O

O
P

P
Q

Q
R

R
S

S
T

U
X

ATP-dependent Clp protease ATP-binding subunit ClpC1

ATP-dependent Clp protease proteolytic subunit 2

ATP-dependent Clp protease proteolytic subunit 1

Unknown peptide

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