SMTL ID : 6oaa.1

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-1-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: D.488, V.489, G.490, P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666, Q.670, G.694, L.698 Chain B: R.645, R.648 Ligands: BEF.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.490, A:G.491, A:G.531, A:G.533, A:G.533, A:T.535, A:T.535, A:L.536 Salt bridges: A:K.534, B:R.645, B:R.645, B:R.648 ADP.4: 17 residues within 4Å: Chain A: I.216, G.217, P.257, G.258, T.259, G.260, K.261, T.262, L.263, V.390, G.418, A.419, A.422 Chain B: D.343, R.369, F.370 Ligands: BEF.2 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.217, A:G.217, A:T.259, A:G.260, A:K.261, A:T.262 Salt bridges: B:R.369, B:R.369 ADP.7: 16 residues within 4Å: Chain B: I.216, G.217, T.259, G.260, K.261, T.262, L.263, V.390, H.394, G.418, A.419, A.422 Chain C: D.343, R.369, F.370 Ligands: BEF.5 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.217, B:G.217, B:T.259, B:G.260, B:T.262, C:R.369 Salt bridges: B:K.261, B:K.261, C:R.369 pi-Stacking: B:H.394 ADP.8: 15 residues within 4Å: Chain B: P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666, G.694, A.695, L.698 Chain C: D.619, R.645, R.648 Ligands: BEF.6 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.531, B:T.532, B:G.533, B:K.534, B:K.534, B:T.535, B:T.535, B:L.536, B:G.694, C:R.645, C:R.645 Salt bridges: B:K.534, B:K.534, C:R.645, C:R.648 ADP.11: 14 residues within 4Å: Chain C: P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666, Q.670, G.694, A.695 Chain D: R.645, R.648 Ligands: BEF.10 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.531, C:T.532, C:G.533, C:K.534, C:L.536, C:Q.670, D:R.645 Salt bridges: D:R.645, D:R.645, D:R.648 ADP.12: 16 residues within 4Å: Chain C: I.216, G.217, G.258, T.259, G.260, K.261, T.262, L.263, V.390, G.418, A.419, A.422 Chain D: D.343, R.369, F.370 Ligands: BEF.9 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.216, C:G.258, C:T.259, C:G.260, C:K.261, C:T.262, C:L.263 Salt bridges: C:K.261, D:R.369, D:R.369 ADP.13: 9 residues within 4Å: Chain D: G.531, T.532, G.533, K.534, T.535, L.536, P.658, I.666, Q.670 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.531, D:G.533, D:K.534, D:T.535, D:T.535, D:L.536 ADP.14: 11 residues within 4Å: Chain D: D.215, I.216, G.258, T.259, G.260, L.263, M.264, V.390, G.418, A.419, A.422 No protein-ligand interaction detected (PLIP)

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)(Covalent)

BEF.2: 6 residues within 4Å: Chain A: T.262, D.314, E.315, A.356 Chain B: R.372 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) BEF.3: 7 residues within 4Å: Chain A: K.534, T.535, D.587, E.588, A.632 Chain B: R.648 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) BEF.5: 7 residues within 4Å: Chain B: P.257, K.261, T.262, E.315 Chain C: D.343, R.372 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) BEF.6: 5 residues within 4Å: Chain B: T.535, D.587, E.588 Chain C: R.648 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) BEF.9: 5 residues within 4Å: Chain C: K.261, T.262, D.314 Chain D: R.369 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) BEF.10: 8 residues within 4Å: Chain C: K.534, T.535, D.587, E.588, A.632 Chain D: D.619, R.648 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Twomey, E.C. et al., Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science (2019)

Release Date

2019-07-03

Peptides

Cell division control protein 48: ABCD
Nuclear protein localization protein 4: E
Ubiquitin: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
G

F
H

Cell division control protein 48

Nuclear protein localization protein 4

Ubiquitin

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