SMTL ID : 8a8w.1

Mycobacterium tuberculosis ClpC1 hexamer structure bound to the natural product antibiotic Ecumycin (class 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: P.189, V.190, I.191, R.193, P.218, G.219, V.220, G.221, K.222, T.223, A.224, I.358, P.396, I.400 Chain F: R.340 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain A Salt bridges: F:R.340, F:R.340, A:K.222 Hydrogen bonds: A:I.191, A:I.191, A:G.219, A:V.220, A:G.221, A:K.222, A:T.223, A:T.223, A:T.223, A:A.224 ADP.2: 19 residues within 4Å: Chain A: R.314, R.340, R.341 Chain B: D.188, P.189, V.190, I.191, P.218, G.219, V.220, G.221, K.222, T.223, A.224, I.358, L.362, P.396, D.397, I.400 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.188, B:I.191, B:I.191, B:G.219, B:G.221, B:K.222, B:T.223, B:T.223, B:T.223, A:R.314 Salt bridges: B:K.222, B:K.222, A:R.314, A:R.340, A:R.340, A:R.341 ADP.3: 16 residues within 4Å: Chain B: R.517, I.518, I.519, P.554, S.555, G.556, V.557, G.558, K.559, T.560, E.561, M.730, L.733, A.770, R.771, R.774 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.517, B:I.519, B:G.556, B:V.557, B:G.558, B:T.560, B:T.560, B:T.560, B:E.561, B:E.561, B:R.771, B:R.774 Salt bridges: B:K.559 ADP.4: 16 residues within 4Å: Chain B: R.314, R.340, R.341 Chain C: D.188, P.189, V.190, I.191, G.219, V.220, G.221, K.222, T.223, A.224, I.358, P.396, I.400 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:D.188, C:I.191, C:I.191, C:G.219, C:V.220, C:G.221, C:K.222, C:T.223, C:T.223, C:A.224, B:R.314, B:R.314 Salt bridges: C:K.222, C:K.222, B:R.340, B:R.340, B:R.341 ADP.5: 19 residues within 4Å: Chain B: E.643, R.712 Chain C: R.517, I.518, I.519, P.554, S.555, G.556, V.557, G.558, K.559, T.560, E.561, K.564, E.626, M.730, L.733, A.770, R.771 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.519, C:G.556, C:V.557, C:G.558, C:K.559, C:T.560, C:T.560, C:E.561, C:E.626, C:E.626, C:R.771 Salt bridges: C:K.559, C:K.559, B:R.712 ADP.6: 16 residues within 4Å: Chain C: R.314, R.340, R.341 Chain D: D.188, P.189, V.190, I.191, R.193, P.218, G.219, V.220, G.221, K.222, T.223, I.358, L.362 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:R.314, C:R.314, D:D.188, D:I.191, D:I.191, D:G.219, D:G.221, D:K.222, D:T.223 Salt bridges: C:R.340, C:R.340, C:R.341, D:K.222 ADP.7: 15 residues within 4Å: Chain C: R.712 Chain D: R.517, I.518, I.519, S.555, G.556, V.557, G.558, K.559, T.560, E.561, M.730, A.770, R.771, R.774 14 PLIP interactions: 1 interactions with chain C, 13 interactions with chain D Salt bridges: C:R.712, D:K.559, D:R.771, D:R.771 Hydrogen bonds: D:I.519, D:I.519, D:G.556, D:V.557, D:G.558, D:K.559, D:T.560, D:T.560, D:T.560, D:R.774 ADP.8: 18 residues within 4Å: Chain D: A.313, R.314, R.340, R.341 Chain E: P.189, V.190, I.191, R.193, P.218, G.219, G.221, K.222, T.223, A.224, I.358, L.362, P.396, I.400 14 PLIP interactions: 8 interactions with chain E, 6 interactions with chain D Hydrogen bonds: E:D.188, E:I.191, E:I.191, E:G.219, E:K.222, E:T.223, E:T.223, D:R.314, D:R.314, D:R.341 Salt bridges: E:K.222, D:R.314, D:R.340, D:R.340 ADP.9: 16 residues within 4Å: Chain D: E.643, R.712 Chain E: R.517, I.518, I.519, S.555, G.556, V.557, G.558, K.559, T.560, E.561, N.667, M.730, R.771, R.774 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:I.519, E:I.519, E:G.556, E:V.557, E:G.558, E:K.559, E:T.560, E:T.560, E:T.560, E:E.561, E:E.561, E:R.774, E:R.774, D:E.643, D:E.643 Salt bridges: E:K.559, E:K.559, E:R.771, E:R.771, D:R.712 ADP.10: 17 residues within 4Å: Chain E: R.340 Chain F: D.188, P.189, V.190, I.191, R.193, G.219, V.220, G.221, K.222, T.223, A.224, H.354, I.358, L.362, P.396, D.397 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:D.188, F:I.191, F:I.191, F:G.219, F:V.220, F:G.221, F:K.222, F:T.223, E:R.340, E:R.340 Salt bridges: E:R.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weinhaupl, K. et al., Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action. J.Biol.Chem. (2022)

Release Date

2022-10-26

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpC1: ABCDEF
Bound polypeptide: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP-dependent Clp protease ATP-binding subunit ClpC1

Bound polypeptide

Related Entries With Identical Sequence