SMTL ID : 7uj0.1

ClpAP complex bound to ClpS N-terminal extension, class IIIb

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-7-mer

Ligands

7 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 17 residues within 4Å: Chain A: 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 Chain B: R.206, R.339 Ligands: MG.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.217, A:V.218, A:G.219, A:K.220, A:T.221, A:A.222, B:R.339 AGS.5: 22 residues within 4Å: Chain B: D.186, 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 Chain C: R.206, A.336, R.339, R.340 Ligands: MG.7 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:I.189, B:I.189, B:S.216, B:S.216, B:G.217, B:G.219, B:T.221, B:T.221, B:T.221, B:A.222, C:R.339, C:R.339, C:R.340, C:R.340 Salt bridges: C:R.339, C:R.339, C:R.340 AGS.6: 23 residues within 4Å: Chain B: L.459, V.460, F.461, Q.463, T.497, G.498, V.499, G.500, K.501, T.502, E.503, E.565, N.606, L.653, V.661, K.664, F.665, A.701, R.702 Chain C: D.582, E.639, R.643 Ligands: MG.8 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:F.461, B:F.461, B:G.498, B:G.500, B:K.501, B:T.502, B:E.503, B:E.565, B:N.606, B:K.664, B:R.702, C:R.643, C:R.643 Salt bridges: B:K.501, B:R.702, B:R.702 AGS.9: 24 residues within 4Å: Chain C: D.186, P.187, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, E.286, T.323, I.357, L.361, P.395, D.396, I.399 Chain D: R.206, A.336, R.339, R.340 Ligands: MG.11 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:D.186, C:I.189, C:I.189, C:R.191, C:G.217, C:V.218, C:G.219, C:K.220, C:K.220, C:T.221, C:A.222, D:R.206, D:R.339, D:R.340 Salt bridges: C:K.220, D:R.339, D:R.339 AGS.10: 25 residues within 4Å: Chain C: L.459, V.460, F.461, Q.463, P.496, T.497, G.498, V.499, G.500, K.501, T.502, E.503, E.565, T.604, N.606, L.653, V.661, K.664, F.665, A.701, R.702 Chain D: D.582, E.639, R.643 Ligands: MG.12 16 PLIP interactions: 2 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:R.643, D:R.643, C:F.461, C:G.498, C:V.499, C:V.499, C:G.500, C:K.501, C:K.501, C:T.502, C:E.503, C:N.606, C:K.664, C:R.702 Salt bridges: C:K.501, C:R.702 AGS.13: 24 residues within 4Å: Chain D: P.187, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, E.286, S.321, T.323, I.357, L.361, Y.365, P.395, I.399 Chain E: R.206, A.336, R.339, R.340 Ligands: MG.15 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:I.189, D:I.189, D:G.217, D:G.219, D:G.219, D:K.220, D:K.220, D:T.221, D:A.222, D:S.321, D:T.323, E:R.339 Salt bridges: D:K.220, D:K.220, E:R.339, E:R.339, E:R.340 AGS.14: 22 residues within 4Å: Chain D: L.459, V.460, F.461, Q.463, T.497, G.498, V.499, G.500, K.501, T.502, E.503, N.606, L.653, V.661, K.664, F.665, A.701, R.702 Chain E: K.486, E.639, R.643 Ligands: MG.16 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:F.461, D:F.461, D:G.498, D:V.499, D:G.500, D:K.501, D:T.502, D:E.503, D:K.664, D:R.702, D:R.702, E:R.643, E:R.643 Salt bridges: D:K.501, D:R.702

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

ADP.2: 16 residues within 4Å: Chain A: L.459, V.460, F.461, T.497, G.498, G.500, T.502, E.503, L.653, V.661, K.664, F.665, A.701, R.702 Chain B: R.643 Ligands: MG.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.461, A:F.461, A:G.500, A:K.664, B:R.643 Salt bridges: A:R.702, A:R.702 ADP.17: 21 residues within 4Å: Chain E: D.186, P.187, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, E.286, I.357, L.361, P.395, D.396, I.399 Chain F: R.206, R.339 Ligands: MG.19 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:I.189, E:I.189, E:G.217, E:V.218, E:G.219, E:K.220, E:T.221 Salt bridges: E:K.220, F:R.339 ADP.18: 18 residues within 4Å: Chain E: L.459, V.460, F.461, Q.463, T.497, G.498, V.499, G.500, K.501, T.502, E.503, L.653, V.661, K.664, F.665, A.701, R.702, A.705 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:F.461, E:F.461, E:G.498, E:G.500, E:K.501, E:T.502, E:T.502, E:E.503, E:E.503, E:K.664 Salt bridges: E:K.501, E:R.702, E:R.702 ADP.20: 20 residues within 4Å: Chain A: R.335, R.339 Chain F: D.186, P.187, L.188, I.189, G.190, 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 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:D.186, F:D.186, F:I.189, F:I.189, F:G.217, F:G.219, F:K.220, F:T.221, F:T.221, F:A.222 Salt bridges: F:K.220, A:R.335, A:R.339, A:R.339 ADP.21: 15 residues within 4Å: Chain F: V.460, F.461, G.462, Q.463, G.498, V.499, G.500, T.502, E.503, R.518, L.653, K.664, F.665, A.701, R.702 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.462, F:G.500, F:E.503, F:E.503

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.221, D.285 Chain B: R.339 Ligands: AGS.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.221, A:D.285 MG.4: 6 residues within 4Å: Chain A: G.498, V.499, G.500, T.502, E.503 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: T.221, D.285 Chain C: R.340 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.221 MG.8: 5 residues within 4Å: Chain B: T.502, D.564, T.604 Chain C: R.643 Ligands: AGS.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.502, B:D.564 MG.11: 5 residues within 4Å: Chain C: T.221, D.285, S.321 Chain D: R.340 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.221 MG.12: 5 residues within 4Å: Chain C: T.502, E.565, T.604 Chain D: R.643 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.502 MG.15: 6 residues within 4Å: Chain D: T.221, D.285, E.286, S.321 Chain E: R.340 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.221 MG.16: 4 residues within 4Å: Chain D: T.502, T.604 Chain E: R.643 Ligands: AGS.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.502 MG.19: 3 residues within 4Å: Chain E: T.221, D.285 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., AAA+ protease-adaptor structures reveal altered conformations and ring specialization. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-11-09

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpA: ABCDEF
ATP-dependent Clp protease adapter protein ClpS: G
ATP-dependent Clp protease proteolytic subunit: HIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
S

H
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease ATP-binding subunit ClpA

ATP-dependent Clp protease adapter protein ClpS

ATP-dependent Clp protease proteolytic subunit

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