SMTL ID : 6oab.1

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-5-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: I.216, G.217, G.258, T.259, G.260, K.261, T.262, L.263, V.390, H.394, G.418 Chain B: R.369, R.372 Ligands: BEF.2 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.372, A:G.217, A:G.258, A:T.259, A:G.260, A:K.261, A:T.262, A:T.262, A:L.263 Salt bridges: B:R.369, B:R.369, A:K.261, A:K.261 ADP.4: 13 residues within 4Å: Chain A: D.488, V.489, G.531, T.532, G.533, K.534, T.535, L.536, Q.670 Chain B: D.619, R.645, R.648 Ligands: BEF.3 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:D.619, B:R.645, A:G.531, A:T.532, A:G.533, A:K.534, A:T.535, A:L.536, A:Q.670 Salt bridges: B:R.645, B:R.645, B:R.648, A:K.534 ADP.5: 9 residues within 4Å: Chain B: G.490, P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.531, B:T.532, B:G.533, B:K.534, B:T.535, B:T.535 ADP.6: 11 residues within 4Å: Chain B: I.216, T.259, G.260, K.261, T.262, L.263, M.264, V.390, G.418, A.419, A.422 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.261, B:T.262, B:T.262, B:T.262, B:L.263 ADP.7: 18 residues within 4Å: Chain C: 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, A.695 Chain D: D.619, R.645, R.648 Ligands: BEF.10 13 PLIP interactions: 4 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:D.619, C:G.490, C:G.531, C:G.533, C:G.533, C:T.535, C:T.535, C:L.536, C:Q.670 Salt bridges: D:R.645, D:R.645, D:R.648, C:K.534 ADP.11: 13 residues within 4Å: Chain C: I.216, G.217, P.257, G.260, K.261, T.262, L.263, G.418, A.422 Chain D: R.369, F.370, R.372 Ligands: BEF.9 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.217, C:G.217, C:K.261, C:T.262, C:T.262, D:R.372 Salt bridges: D:R.369, D:R.369 ADP.12: 17 residues within 4Å: Chain A: D.343, R.369, R.372 Chain D: I.216, G.217, P.257, G.258, T.259, G.260, K.261, T.262, L.263, V.390, I.393, H.394, G.418 Ligands: BEF.14 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.217, D:G.217, D:G.258, D:T.259, D:G.260, D:K.261, D:T.262, D:L.263, D:H.394 Salt bridges: D:K.261, D:K.261, A:R.369, A:R.372 ADP.13: 16 residues within 4Å: Chain A: R.645, R.648 Chain D: 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 Ligands: BEF.15 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.490, D:G.490, D:G.531, D:T.532, D:G.533, D:K.534, D:L.536, D:Q.670 Salt bridges: D:K.534, D:K.534, A:R.645, A:R.648 ADP.16: 16 residues within 4Å: Chain C: D.619, R.645, R.648 Chain E: V.489, G.490, G.531, T.532, G.533, K.534, T.535, L.536, I.666, Q.670, G.694, A.695 Ligands: BEF.18 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.490, E:G.531, E:T.532, E:G.533, E:K.534, E:T.535, E:L.536, E:L.537, E:Q.670 Salt bridges: C:R.645, C:R.648 ADP.17: 11 residues within 4Å: Chain C: R.369, F.370 Chain E: G.258, T.259, G.260, K.261, T.262, L.263, D.314, V.390 Ligands: BEF.8 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.258, E:T.259, E:K.261, E:T.262, E:L.263 Salt bridges: E:K.261, C:R.369, C:R.369

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

BEF.2: 9 residues within 4Å: Chain A: K.261, T.262, D.314, E.315 Chain B: L.339, D.343, R.369, R.372 Ligands: ADP.1 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.4 No protein-ligand interaction detected (PLIP) BEF.8: 6 residues within 4Å: Chain C: D.343, R.369, R.372 Chain E: D.314, E.315 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) BEF.9: 7 residues within 4Å: Chain C: T.262, D.314, E.315, A.356 Chain D: L.339, R.372 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) BEF.10: 7 residues within 4Å: Chain C: K.534, T.535, D.587, E.588, A.632 Chain D: R.648 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) BEF.14: 8 residues within 4Å: Chain A: D.343, R.372 Chain D: K.261, T.262, D.314, E.315, A.356 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) BEF.15: 6 residues within 4Å: Chain A: R.648 Chain D: K.534, T.535, D.587, E.588 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) BEF.18: 7 residues within 4Å: Chain C: R.648 Chain E: T.535, D.587, E.588, A.632, N.634 Ligands: ADP.16 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: ABCDE
poly(alanine) substrate: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
B

D
C

E
A

F
H

Cell division control protein 48

poly(alanine) substrate

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