SMTL ID : 7uiv.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-7-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: D.186, P.187, L.188, I.189, S.216, G.217, V.218, G.219, K.220, T.221, A.222, I.223, I.357, L.361, R.392, P.395, I.399 Chain B: R.335, R.339 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.189, A:G.217, A:G.219, A:K.220, A:T.221, A:T.221, A:R.392 ADP.13: 21 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: D.582, R.643 Ligands: MG.15 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:F.461, D:G.498, D:V.499, D:G.500, D:K.501, D:T.502, D:T.502, D:T.502, D:E.503, D:E.503 Salt bridges: D:K.501, D:R.702, D:R.702, E:R.643 ADP.16: 20 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, I.357, L.361, Y.365, P.395, D.396, I.399 Chain F: R.206, R.339 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.186, E:I.189, E:I.189, E:R.191, E:G.217, E:V.218, E:G.219, E:K.220, E:T.221, E:T.221, E:T.221 Salt bridges: E:K.220 ADP.18: 18 residues within 4Å: Chain A: R.206, R.339 Chain F: D.186, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, P.349, I.357, L.361, P.395, I.399 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain F Hydrogen bonds: A:R.206, A:R.206, F:D.186, F:S.216, F:G.217, F:G.219, F:T.221, F:A.222 Salt bridges: A:R.339

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

AGS.2: 24 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, N.606, L.653, V.661, K.664, F.665, A.701, R.702 Chain B: D.582, E.639, N.642, R.643 Ligands: MG.3 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.461, A:F.461, A:Q.463, A:G.498, A:V.499, A:G.500, A:K.501, A:T.502, A:E.503, A:N.606, A:K.664, A:R.702, B:R.643 Salt bridges: A:K.501, A:R.702 AGS.4: 27 residues within 4Å: Chain B: D.186, P.187, L.188, I.189, G.190, R.191, E.215, S.216, G.217, G.219, K.220, T.221, A.222, E.286, I.357, L.361, Y.365, P.395, D.396, I.399 Chain C: R.206, K.207, S.312, A.336, R.339, R.340 Ligands: MG.6 15 PLIP interactions: 5 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:R.206, C:R.339, C:R.340, B:D.186, B:I.189, B:I.189, B:G.217, B:G.219, B:K.220, B:K.220, B:T.221, B:T.221, B:A.222 Salt bridges: C:R.339, C:R.339 AGS.5: 25 residues within 4Å: Chain B: 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, N.606, L.653, V.661, K.664, F.665, A.701, R.702 Chain C: D.582, E.639, N.642, R.643 Ligands: MG.7 17 PLIP interactions: 15 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:K.501, B:T.502, B:T.502, B:E.503, B:N.606, B:N.606, B:K.664, B:R.702, C:R.643 Salt bridges: B:R.702, B:R.702, C:R.643 AGS.8: 26 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, S.321, T.323, I.357, L.361, Y.365, P.395, I.399 Chain D: R.206, K.207, A.336, R.339, R.340 Ligands: MG.10 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:D.186, C:I.189, C:I.189, C:G.217, C:G.219, C:G.219, C:K.220, C:T.221, C:A.222, C:E.286, C:E.286, C:E.286, D:R.340, D:R.340 Salt bridges: C:K.220, C:K.220, D:R.339, D:R.339, D:R.340 AGS.9: 27 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.657, V.661, K.664, F.665, A.701, R.702 Chain D: K.486, D.582, E.639, R.643 Ligands: MG.11 15 PLIP interactions: 2 interactions with chain D, 13 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 Salt bridges: C:K.501, C:R.702 AGS.12: 25 residues within 4Å: Chain D: D.186, P.187, L.188, I.189, R.191, S.216, G.217, V.218, G.219, K.220, T.221, A.222, T.323, I.357, L.361, Y.365, P.395, I.399 Chain E: R.206, K.207, S.312, A.336, R.339, R.340 Ligands: MG.14 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:D.186, D:I.189, D:I.189, D:R.191, D:G.217, D:V.218, D:G.219, D:K.220, D:T.221, D:T.221, D:Y.365, D:Y.365, E:R.339, E:R.340, E:R.340 Salt bridges: D:K.220, E:R.339, E:R.339 AGS.17: 19 residues within 4Å: Chain E: V.460, F.461, G.462, Q.463, T.497, G.498, V.499, G.500, K.501, T.502, E.503, R.518, L.653, V.657, V.661, K.664, F.665, A.701, R.702 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:F.461, E:G.498, E:G.500, E:T.502, E:T.502, E:E.503 Salt bridges: E:R.702

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: K.501, T.502, D.564, T.604, N.606 Chain B: R.643 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.502 MG.6: 5 residues within 4Å: Chain B: K.220, T.221, E.286, S.321 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.221 MG.7: 8 residues within 4Å: Chain B: K.501, T.502, D.564, E.565, T.604, N.606 Chain C: R.643 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.502 MG.10: 6 residues within 4Å: Chain C: T.221, D.285, E.286, S.321 Chain D: R.340 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.221 MG.11: 5 residues within 4Å: Chain C: T.502, D.564, E.565, T.604 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.502 MG.14: 5 residues within 4Å: Chain D: T.221, D.285, E.286 Chain E: R.340 Ligands: AGS.12 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain D: K.501, T.502, T.604 Chain E: R.643 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.502

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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