SMTL ID : 6w20.1

ClpAP Disengaged State bound to RepA-GFP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-6-1-mer

Ligands

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

ADP.1: 20 residues within 4Å: Chain O: D.186, P.187, L.188, I.189, R.191, E.215, S.216, G.217, V.218, G.219, K.220, T.221, E.286, I.357, L.361, P.395, D.396, I.399 Chain T: R.335, R.339 17 PLIP interactions: 14 interactions with chain O, 3 interactions with chain T Hydrogen bonds: O:D.186, O:I.189, O:I.189, O:E.215, O:G.217, O:V.218, O:G.219, O:K.220, O:T.221, O:T.221, O:T.221, O:E.286, O:D.396, O:D.396 Salt bridges: T:R.335, T:R.339, T:R.339 ADP.2: 16 residues within 4Å: Chain O: 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 11 PLIP interactions: 11 interactions with chain O Hydrogen bonds: O:F.461, O:G.498, O:V.499, O:V.499, O:G.500, O:K.501, O:T.502, O:T.502, O:T.502, O:E.503 Salt bridges: O:R.702 ADP.11: 12 residues within 4Å: Chain T: F.461, T.497, G.498, V.499, G.500, K.501, T.502, D.564, L.653, V.657, V.661, K.664 10 PLIP interactions: 10 interactions with chain T Hydrogen bonds: T:F.461, T:F.461, T:G.498, T:V.499, T:G.500, T:T.502, T:T.502, T:E.503, T:K.664 Salt bridges: T:R.702

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

ATP.3: 21 residues within 4Å: Chain O: R.339 Chain P: D.186, P.187, L.188, I.189, R.191, E.215, 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 14 PLIP interactions: 11 interactions with chain P, 3 interactions with chain O Hydrogen bonds: P:D.186, P:I.189, P:R.191, P:S.216, P:G.217, P:G.219, P:K.220, P:T.221, P:T.221, P:A.222, O:R.339 Salt bridges: P:K.220, O:R.339, O:R.339 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, K.664, F.665, A.701, R.702 16 PLIP interactions: 15 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, O:R.643 Salt bridges: P:K.501, P:K.501, P:R.702, P:R.702, P:R.702 ATP.5: 21 residues within 4Å: Chain P: A.336, R.339, R.340 Chain Q: 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 17 PLIP interactions: 12 interactions with chain Q, 5 interactions with chain P Hydrogen bonds: Q:D.186, Q:I.189, Q:I.189, Q:G.217, Q:V.218, Q:G.219, Q:G.219, Q:K.220, Q:T.221, Q:A.222, P:R.340 Salt bridges: Q:K.220, Q:K.220, P:R.339, P:R.339, P:R.339, P:R.340 ATP.6: 17 residues within 4Å: Chain P: R.643 Chain Q: V.460, F.461, P.496, T.497, G.498, V.499, G.500, K.501, T.502, E.503, N.606, L.653, V.661, K.664, A.701, R.702 16 PLIP interactions: 15 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:T.502, Q:E.503, Q:E.503, Q:N.606, Q:K.664 Salt bridges: Q:K.501, Q:K.501, Q:R.702, P:R.643 ATP.7: 21 residues within 4Å: Chain Q: A.336, R.339, R.340 Chain R: 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 15 PLIP interactions: 9 interactions with chain R, 6 interactions with chain Q Hydrogen bonds: R:D.186, R:I.189, R:I.189, R:G.217, R:T.221, R:T.221, R:A.222, R:Y.365, Q:A.336 Salt bridges: R:K.220, Q:R.339, Q:R.339, Q:R.339, Q:R.340, Q:R.340 ATP.8: 19 residues within 4Å: Chain Q: E.639, 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, L.653, V.661, K.664, A.701, R.702 19 PLIP interactions: 17 interactions with chain R, 2 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:E.503, R:E.503, R:N.606, R:N.606, R:K.664, Q:E.639 Salt bridges: R:K.501, R:K.501, R:R.702, R:R.702, R:R.702, Q:R.643 ATP.9: 17 residues within 4Å: Chain R: R.339 Chain S: P.187, L.188, I.189, R.191, S.216, G.217, G.219, K.220, T.221, A.222, E.286, I.357, L.361, K.364, P.395, I.399 10 PLIP interactions: 9 interactions with chain S, 1 interactions with chain R Hydrogen bonds: S:I.189, S:I.189, S:G.217, S:G.219, S:K.220, S:T.221, S:A.222, S:E.286, S:K.364 Salt bridges: R:R.339 ATP.10: 20 residues within 4Å: Chain R: D.582, E.639, R.643 Chain S: 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, V.661, K.664, A.701, R.702 20 PLIP interactions: 19 interactions with chain S, 1 interactions with chain R Hydrogen bonds: S:F.461, S:G.498, S:V.499, S:V.499, S:G.500, S:K.501, S:T.502, S:T.502, S:E.503, S:E.503, S:E.565, S:E.565, S:N.606, S:K.664 Salt bridges: S:K.501, S:K.501, S:R.702, S:R.702, S:R.702, R:R.643

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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