SMTL ID : 6w22.1

ClpA Engaged1 State bound to RepA-GFP (ClpA Focused Refinement)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: P.187, L.188, I.189, R.191, E.215, S.216, G.217, V.218, G.219, K.220, T.221, A.222, I.357, L.361, P.395, D.396 Chain F: R.206 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:I.189, A:R.191, A:G.217, A:V.218, A:G.219, A:K.220, A:T.221, A:A.222, A:D.396, F:R.206 Salt bridges: A:K.220, A:K.220 ATP.3: 18 residues within 4Å: Chain A: A.336, R.339, R.340 Chain B: P.187, L.188, I.189, S.216, G.217, V.218, G.219, K.220, T.221, A.222, T.323, I.357, P.395, D.396, I.399 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:I.189, B:G.217, B:G.219, B:K.220, B:T.221, B:T.221, B:A.222, A:A.336 Salt bridges: B:K.220, B:K.220, A:R.339, A:R.339, A:R.339, A:R.340, A:R.340 ATP.4: 15 residues within 4Å: Chain A: R.643 Chain B: L.459, V.460, F.461, T.497, G.498, V.499, G.500, K.501, T.502, E.503, E.565, V.661, K.664, R.702 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.461, B:G.498, B:V.499, B:V.499, B:G.500, B:K.501, B:T.502, B:T.502, B:E.503, B:E.503, B:K.664 Salt bridges: B:K.501, B:K.501, B:R.702, B:R.702, B:R.702, A:R.643 ATP.5: 18 residues within 4Å: Chain B: R.339, R.340 Chain C: P.187, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, I.357, L.361, P.395, D.396, I.399 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:I.189, C:I.189, C:G.217, C:V.218, C:G.219, C:K.220, C:T.221, C:T.221, C:T.221, C:A.222, C:D.396, C:D.396, B:A.336 Salt bridges: C:K.220, C:K.220, B:R.339, B:R.339, B:R.340 ATP.6: 19 residues within 4Å: Chain B: E.639, R.643 Chain C: L.459, V.460, F.461, T.497, G.498, V.499, G.500, K.501, T.502, E.503, E.565, N.606, V.661, K.664, F.665, A.701, R.702 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.461, C:F.461, C:G.498, C:V.499, C:G.500, C:K.501, C:T.502, C:E.503, C:E.565, C:E.565, C:N.606, C:K.664, C:K.664 Salt bridges: C:K.501, C:K.501, C:R.702, C:R.702, B:R.643 ATP.7: 17 residues within 4Å: Chain C: R.339, R.340 Chain D: P.187, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, I.357, L.361, P.395, I.399 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:I.189, D:I.189, D:S.216, D:G.217, D:G.219, D:T.221, D:T.221, D:A.222, C:R.340 Salt bridges: D:K.220, D:K.220, C:R.339, C:R.339, C:R.339, C:R.340 ATP.8: 18 residues within 4Å: Chain C: R.643 Chain D: L.459, V.460, F.461, T.497, G.498, V.499, G.500, K.501, T.502, E.503, E.565, N.606, V.661, K.664, F.665, A.701, R.702 19 PLIP interactions: 1 interactions with chain C, 18 interactions with chain D Salt bridges: C:R.643, D:K.501, D:K.501, D:R.702, D:R.702, D:R.702 Hydrogen bonds: D:F.461, D:F.461, D:G.498, D:G.500, D:K.501, D:T.502, D:T.502, D:T.502, D:E.503, D:E.503, D:E.565, D:N.606, D:K.664 ATP.10: 17 residues within 4Å: Chain D: D.582, R.643 Chain E: L.459, V.460, F.461, T.497, G.498, V.499, G.500, K.501, T.502, E.503, N.606, V.661, K.664, A.701, R.702 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:F.461, E:G.498, E:V.499, E:G.500, E:K.501, E:T.502, E:T.502, E:E.503, E:E.503, E:N.606, E:K.664 Salt bridges: E:K.501, E:K.501, E:R.702, E:R.702, D:R.643

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

ADP.2: 17 residues within 4Å: Chain A: L.459, V.460, F.461, Q.463, P.496, T.497, G.498, V.499, G.500, K.501, T.502, E.503, L.653, V.661, F.665, A.701, R.702 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:F.461, A:F.461, A:G.498, A:V.499, A:G.500, A:K.501, A:T.502, A:T.502, A:T.502, A:E.503, A:E.503 Salt bridges: A:K.501, A:R.702 ADP.9: 15 residues within 4Å: Chain E: L.188, I.189, R.191, E.215, S.216, G.217, V.218, G.219, K.220, A.222, I.357, L.361, P.395, D.396, I.399 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:I.189, E:R.191, E:S.216, E:G.217, E:G.219 Salt bridges: E:K.220, E:K.220 ADP.11: 13 residues within 4Å: Chain E: R.339 Chain F: L.188, E.215, S.216, G.217, V.218, G.219, K.220, T.221, A.222, I.357, P.395, D.396 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.216, F:G.217, F:T.221 Salt bridges: F:K.220, E:R.339, E:R.339 ADP.12: 12 residues within 4Å: Chain F: L.459, V.460, F.461, G.498, V.499, G.500, T.502, E.503, V.661, F.665, A.701, R.702 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:F.461, F:G.498, F:V.499, F:T.502, F:T.502, F:E.503 Salt bridges: F:R.702

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez, K.E. et al., Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-04-29

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpA: ABCDEF
RepA, green fluorescent protein fusion: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
X

ATP-dependent Clp protease ATP-binding subunit ClpA

RepA, green fluorescent protein fusion

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