SMTL ID : 6vfx.1

ClpXP from Neisseria meningitidis - Conformation B

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-14-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK: Unidentified peptide substrate(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 23 residues within 4Å: Chain A: G.152, Y.153, V.154, V.202 Chain B: G.152, Y.153, V.154 Chain C: G.152, Y.153, V.154, H.230, N.232 Chain E: G.152, Y.153, V.154, V.202 Chain F: Y.153, V.154, N.195, P.196, S.197, I.198, T.199 16 PLIP interactions: 6 interactions with chain F, 3 interactions with chain B, 4 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: F:I.198, B:Y.153, B:V.154, E:Y.153, E:Y.153, E:V.154, A:V.154 Hydrogen bonds: F:N.195, F:S.197, F:I.198, F:I.198, F:T.199, B:G.152, E:V.154, A:G.152, A:V.154

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

ATP.2: 24 residues within 4Å: Chain A: H.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, Q.185, A.250, L.316, I.324, P.328, A.368, R.369 Chain E: S.111, E.216, E.302, R.306 Ligands: MG.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:I.79, A:Q.81, A:G.122, A:S.123, A:S.123, A:S.123, A:G.124, A:K.125, A:T.126, A:L.127, A:Q.185, E:E.302 Salt bridges: A:K.125, A:K.125, A:R.369, A:R.369, A:R.369, E:R.306 ATP.4: 23 residues within 4Å: Chain A: E.216, E.302, R.306 Chain B: H.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, Q.185, A.250, L.316, I.324, P.328, A.368, R.369 Ligands: MG.5 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.79, B:G.122, B:S.123, B:S.123, B:S.123, B:G.124, B:G.124, B:K.125, B:T.126, B:L.127, B:Q.185, A:E.302 Salt bridges: B:K.125, B:K.125, B:R.369, B:R.369, B:R.369, A:R.306 ATP.6: 21 residues within 4Å: Chain C: H.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, Q.185, A.250, L.316, I.324, P.328, A.368, R.369 Chain D: E.302 Ligands: MG.7 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.79, C:G.122, C:S.123, C:S.123, C:S.123, C:G.124, C:G.124, C:K.125, C:T.126, C:L.127, C:Q.185, D:E.302 Salt bridges: C:K.125, C:K.125, C:R.369, C:R.369 ATP.9: 23 residues within 4Å: Chain C: E.216, E.302, R.306 Chain E: H.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, Q.185, A.250, L.316, I.324, P.328, A.368, R.369 Ligands: MG.10 18 PLIP interactions: 16 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:I.79, E:G.122, E:S.123, E:S.123, E:S.123, E:G.124, E:G.124, E:K.125, E:T.126, E:L.127, E:Q.185, C:E.302 Salt bridges: E:K.125, E:K.125, E:R.369, E:R.369, E:R.369, C:R.306 ATP.11: 21 residues within 4Å: Chain B: E.216, E.302, R.306 Chain F: H.77, V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, A.250, L.316, I.324, P.328, A.368, R.369 Ligands: MG.12 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:I.79, F:T.121, F:G.122, F:S.123, F:S.123, F:S.123, F:G.124, F:K.125, F:T.126, F:L.127, B:E.302, B:E.302 Salt bridges: F:K.125, F:K.125, F:R.369, F:R.369, F:R.369, B:R.306

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: T.126, D.184, Q.185 Chain E: K.213, R.306 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.126, A:D.184 MG.5: 5 residues within 4Å: Chain A: R.306 Chain B: T.126, D.184, Q.185 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.126, B:D.184 MG.7: 4 residues within 4Å: Chain C: T.126, D.184, R.369 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.126 MG.10: 8 residues within 4Å: Chain C: K.213, E.216, R.306 Chain E: T.126, Y.182, D.184, Q.185 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.126, E:D.184 MG.12: 4 residues within 4Å: Chain B: R.306 Chain F: T.126, D.184 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.126, F:D.184

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

ADP.8: 18 residues within 4Å: Chain D: H.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, L.316, I.324, P.328, N.330, A.368, R.369 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:I.79, D:P.120, D:G.122, D:S.123, D:S.123, D:S.123, D:G.124, D:K.125, D:T.126, D:T.126, D:L.127 Salt bridges: D:K.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ripstein, Z.A. et al., A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery. Elife (2020)

Release Date

2020-01-22

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEF
ATP-dependent Clp protease proteolytic subunit: GHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
E

D
F

E
D

F
A

G
L

H
O

I
P

J
Q

K
R

L
S

M
T

N
U

O
H

P
I

Q
J

R
K

S
M

T
N

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

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