SMTL ID : 6uqo.1

ClpA/ClpP Engaged State bound to RepA-GFP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-14-mer

Ligands

2 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: RepA-GFP(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 13 residues within 4Å: Chain A: K.90, Y.91, R.92 Chain B: Y.91, R.92 Chain C: K.90, Y.91, R.92, A.127, A.128 Chain D: K.90, Y.91, R.92 6 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:A.127, D:K.90, A:Y.91 Hydrogen bonds: D:K.90, D:R.92, B:R.92 UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.2: 12 residues within 4Å: Chain A: G.371, Y.372, V.373 Chain B: G.371, Y.372, V.373 Chain C: G.371, Y.372, V.373 Chain D: G.371, Y.372, V.373 10 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:Y.372, C:V.373, A:V.373, B:Y.372, B:V.373, D:Y.372, D:V.373 Hydrogen bonds: C:V.373, A:V.373, B:V.373

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

ADP.3: 15 residues within 4Å: Chain A: P.19, L.20, I.21, R.23, S.48, G.49, V.50, G.51, K.52, T.53, A.54, I.189, L.193, P.227 Chain F: R.171 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:I.21, A:I.21, A:G.49, A:V.50, A:G.51, A:T.53, A:T.53, A:T.53, A:A.54 Salt bridges: A:K.52, F:R.171, F:R.171 ADP.4: 13 residues within 4Å: Chain A: V.292, F.293, T.329, G.330, V.331, G.332, K.333, T.334, E.335, L.485, V.493, F.497, R.534 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:F.293, A:F.293, A:G.330, A:V.331, A:G.332, A:K.333, A:T.334, A:E.335, A:R.534 Salt bridges: A:K.333, A:R.534, A:R.534 ADP.11: 11 residues within 4Å: Chain E: I.21, R.23, V.50, G.51, K.52, T.53, A.54, D.117, P.181, I.189, P.227 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:I.21, E:I.21, E:T.53, E:A.54 Salt bridges: E:K.52 ADP.13: 14 residues within 4Å: Chain F: P.19, L.20, I.21, G.22, R.23, E.47, S.48, G.49, V.50, G.51, K.52, T.53, I.189, D.228 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:I.21, F:R.23, F:R.23, F:E.47, F:E.47, F:S.48, F:G.49, F:V.50, F:G.51, F:K.52, F:T.53, F:R.224, F:D.228 Salt bridges: F:K.52, F:K.52 ADP.14: 13 residues within 4Å: Chain F: L.291, V.292, F.293, T.329, G.330, V.331, G.332, T.334, L.485, V.493, F.497, A.533, R.534 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:L.291, F:F.293, F:G.330, F:K.333, F:T.334, F:A.533

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

AGS.5: 18 residues within 4Å: Chain A: A.168, R.171, R.172 Chain B: P.19, L.20, I.21, R.23, S.48, G.49, V.50, G.51, K.52, T.53, A.54, T.155, I.189, L.193, I.231 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:I.21, B:I.21, B:V.50, B:G.51, B:K.52, B:T.53, B:T.53, B:T.53, B:A.54, A:R.171, A:R.172 Salt bridges: B:K.52, A:R.171, A:R.171, A:R.172 AGS.6: 16 residues within 4Å: Chain A: R.475 Chain B: L.291, V.292, F.293, T.329, G.330, V.331, G.332, K.333, T.334, E.335, L.485, K.496, F.497, A.533, R.534 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.293, B:F.293, B:G.330, B:V.331, B:G.332, B:K.333, B:T.334, B:T.334, B:E.335, B:K.496, B:A.533, B:R.534, A:R.475, A:R.475 Salt bridges: B:K.333, B:R.534, B:R.534 AGS.7: 19 residues within 4Å: Chain B: A.168, R.171, R.172 Chain C: P.19, L.20, I.21, R.23, S.48, G.49, V.50, G.51, K.52, T.53, A.54, T.155, I.189, L.193, P.227, I.231 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:I.21, C:I.21, C:G.49, C:V.50, C:G.51, C:K.52, C:T.53, C:T.53, C:T.53, C:A.54, B:R.172, B:R.172 Salt bridges: C:K.52, B:R.171, B:R.171 AGS.8: 17 residues within 4Å: Chain B: R.475 Chain C: L.291, V.292, F.293, T.329, G.330, V.331, G.332, K.333, T.334, E.335, E.397, N.438, L.485, K.496, A.533, R.534 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.293, C:F.293, C:Q.295, C:G.330, C:V.331, C:G.332, C:G.332, C:K.333, C:T.334, C:E.335, C:K.496, C:A.533, C:R.534, C:R.534, B:R.475 Salt bridges: C:K.333, C:R.534, C:R.534 AGS.9: 17 residues within 4Å: Chain C: R.171, R.172 Chain D: P.19, L.20, I.21, R.23, S.48, G.49, V.50, G.51, K.52, T.53, A.54, I.189, L.193, D.228, I.231 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:I.21, D:I.21, D:G.49, D:G.51, D:G.51, D:K.52, D:T.53, D:T.53, D:A.54, D:D.228, C:R.171, C:R.172, C:R.172 Salt bridges: D:K.52, C:R.171, C:R.171 AGS.10: 17 residues within 4Å: Chain C: R.475 Chain D: L.291, V.292, F.293, T.329, G.330, V.331, G.332, K.333, T.334, E.335, E.397, N.438, V.493, K.496, F.497, R.534 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:F.293, D:F.293, D:T.329, D:G.330, D:K.333, D:T.334, D:T.334, D:E.335, D:N.438, D:K.496, D:K.496, C:R.475, C:R.475 Salt bridges: D:K.333, D:R.534, D:R.534 AGS.12: 17 residues within 4Å: Chain D: N.474, R.475 Chain E: L.291, V.292, F.293, T.329, G.330, V.331, G.332, K.333, T.334, E.335, N.438, L.485, K.496, A.533, R.534 18 PLIP interactions: 16 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:F.293, E:F.293, E:G.330, E:V.331, E:G.332, E:K.333, E:K.333, E:T.334, E:T.334, E:E.335, E:E.335, E:N.438, E:K.496, D:R.475, D:R.475 Salt bridges: E:K.333, E:R.534, E:R.534

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

2020-04-22

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpA: ABCDEF
ATP-dependent Clp endopeptidase proteolytic subunit ClpP: GHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

ATP-dependent Clp protease ATP-binding subunit ClpA

ATP-dependent Clp endopeptidase proteolytic subunit ClpP

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