SMTL ID : 6w1z.1

ClpAP Engaged1 State bound to RepA-GFP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-6-1-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain O: 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 T: R.206 12 PLIP interactions: 11 interactions with chain O, 1 interactions with chain T Hydrogen bonds: O:I.189, O:R.191, O:G.217, O:V.218, O:G.219, O:K.220, O:T.221, O:A.222, O:D.396, T:R.206 Salt bridges: O:K.220, O:K.220 ATP.3: 18 residues within 4Å: Chain O: A.336, R.339, R.340 Chain P: 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 P, 6 interactions with chain O Hydrogen bonds: P:I.189, P:G.217, P:G.219, P:K.220, P:T.221, P:T.221, P:A.222, O:A.336 Salt bridges: P:K.220, P:K.220, O:R.339, O:R.339, O:R.339, O:R.340, O:R.340 ATP.4: 15 residues within 4Å: Chain O: R.643 Chain P: 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 P, 1 interactions with chain O Hydrogen bonds: P:F.461, P:G.498, P:V.499, P:V.499, P:G.500, P:K.501, P:T.502, P:T.502, P:E.503, P:E.503, P:K.664 Salt bridges: P:K.501, P:K.501, P:R.702, P:R.702, P:R.702, O:R.643 ATP.5: 18 residues within 4Å: Chain P: R.339, R.340 Chain Q: 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 Q, 4 interactions with chain P Hydrogen bonds: Q:I.189, Q:I.189, Q:G.217, Q:V.218, Q:G.219, Q:K.220, Q:T.221, Q:T.221, Q:T.221, Q:A.222, Q:D.396, Q:D.396, P:A.336 Salt bridges: Q:K.220, Q:K.220, P:R.339, P:R.339, P:R.340 ATP.6: 19 residues within 4Å: Chain P: E.639, R.643 Chain Q: 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 Q, 1 interactions with chain P Hydrogen bonds: Q:F.461, Q:F.461, Q:G.498, Q:V.499, Q:G.500, Q:K.501, Q:T.502, Q:E.503, Q:E.565, Q:E.565, Q:N.606, Q:K.664, Q:K.664 Salt bridges: Q:K.501, Q:K.501, Q:R.702, Q:R.702, P:R.643 ATP.7: 17 residues within 4Å: Chain Q: R.339, R.340 Chain R: 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: 5 interactions with chain Q, 10 interactions with chain R Hydrogen bonds: Q:R.340, R:I.189, R:I.189, R:S.216, R:G.217, R:G.219, R:T.221, R:T.221, R:A.222 Salt bridges: Q:R.339, Q:R.339, Q:R.339, Q:R.340, R:K.220, R:K.220 ATP.8: 18 residues within 4Å: Chain Q: R.643 Chain R: 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: 18 interactions with chain R, 1 interactions with chain Q Hydrogen bonds: R:F.461, R:F.461, R:G.498, R:G.500, R:K.501, R:T.502, R:T.502, R:T.502, R:E.503, R:E.503, R:E.565, R:N.606, R:K.664 Salt bridges: R:K.501, R:K.501, R:R.702, R:R.702, R:R.702, Q:R.643 ATP.10: 17 residues within 4Å: Chain R: D.582, R.643 Chain S: 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 S, 1 interactions with chain R Hydrogen bonds: S:F.461, S:G.498, S:V.499, S:G.500, S:K.501, S:T.502, S:T.502, S:E.503, S:E.503, S:N.606, S:K.664 Salt bridges: S:K.501, S:K.501, S:R.702, S:R.702, R:R.643

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

ADP.2: 17 residues within 4Å: Chain O: 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 O Hydrogen bonds: O:F.461, O:F.461, O:G.498, O:V.499, O:G.500, O:K.501, O:T.502, O:T.502, O:T.502, O:E.503, O:E.503 Salt bridges: O:K.501, O:R.702 ADP.9: 15 residues within 4Å: Chain S: 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 S Hydrogen bonds: S:I.189, S:R.191, S:S.216, S:G.217, S:G.219 Salt bridges: S:K.220, S:K.220 ADP.11: 13 residues within 4Å: Chain S: R.339 Chain T: 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: 2 interactions with chain S, 4 interactions with chain T Salt bridges: S:R.339, S:R.339, T:K.220 Hydrogen bonds: T:S.216, T:G.217, T:T.221 ADP.12: 12 residues within 4Å: Chain T: 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 T Hydrogen bonds: T:F.461, T:G.498, T:V.499, T:T.502, T:T.502, T:E.503 Salt bridges: T: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

2020-05-06

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN
ATP-dependent Clp protease ATP-binding subunit ClpA: OPQRST
RepA, green fluorescent protein fusion: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

G
M

H
N

I
O

J
P

K
Q

L
R

M
S

N
T

O
A

P
B

Q
C

R
D

S
E

T
F

U
X

ATP-dependent Clp protease proteolytic subunit

ATP-dependent Clp protease ATP-binding subunit ClpA

RepA, green fluorescent protein fusion

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