SMTL ID : 6opc.1

Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-1-mer

Ligands

10 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-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, L.698 Chain B: D.619, R.645 Ligands: BEF.2, MG.3 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.490, A:G.490, A:G.531, A:T.532, A:G.533, A:K.534, A:T.535, A:T.535, A:L.536, A:Q.670 Salt bridges: A:K.534, B:R.645, B:R.645 ADP.4: 16 residues within 4Å: Chain A: D.215, I.216, G.217, G.258, T.259, G.260, K.261, T.262, L.263, V.390, H.394, G.418, A.419 Chain B: D.343 Ligands: BEF.5, MG.6 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.217, A:G.258, A:T.259, A:T.259, A:G.260, A:K.261, A:T.262, A:L.263 Salt bridges: B:R.369, B:R.369 ADP.7: 18 residues within 4Å: Chain B: D.488, G.490, P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666, Q.670, G.694, A.695, L.698 Chain C: D.619, R.645 Ligands: MG.8, BEF.12 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.490, B:G.490, B:G.531, B:T.532, B:G.533, B:K.534, B:T.535, B:T.535, B:L.536, B:Q.670 Salt bridges: B:K.534, C:R.645, C:R.645 ADP.9: 15 residues within 4Å: Chain B: D.215, G.258, T.259, G.260, K.261, T.262, L.263, V.390, H.394, G.418, A.419 Chain C: D.343, R.369 Ligands: BEF.10, MG.11 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.258, B:T.259, B:T.259, B:G.260, B:K.261, B:T.262, B:T.262, B:L.263 Salt bridges: B:K.261, C:R.369, C:R.369 ADP.13: 16 residues within 4Å: Chain C: G.490, G.531, T.532, G.533, K.534, T.535, L.536, I.666, Q.670, G.694, A.695, L.698 Chain D: D.619, R.645 Ligands: BEF.14, MG.15 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.490, C:G.490, C:G.531, C:T.532, C:G.533, C:K.534, C:T.535, C:T.535, C:L.536, C:Q.670 Salt bridges: C:K.534, D:R.645, D:R.645 ADP.16: 16 residues within 4Å: Chain C: D.215, G.217, G.258, T.259, G.260, K.261, T.262, L.263, V.390, H.394, G.418, A.419 Chain D: D.343, R.369 Ligands: BEF.17, MG.18 10 PLIP interactions: 2 interactions with chain D, 8 interactions with chain C Salt bridges: D:R.369, D:R.369, C:K.261 Hydrogen bonds: C:G.258, C:T.259, C:T.259, C:G.260, C:K.261, C:T.262, C:L.263 ADP.19: 17 residues within 4Å: 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 Chain E: D.619, R.645 Ligands: BEF.20, MG.21 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.490, D:G.490, D:G.531, D:T.532, D:G.533, D:K.534, D:T.535, D:T.535, D:L.536, D:Q.670 Salt bridges: D:K.534, E:R.645, E:R.645 ADP.22: 16 residues within 4Å: Chain D: D.215, G.258, T.259, G.260, K.261, T.262, L.263, V.390, H.394, G.418, A.419 Chain E: D.343, R.369, R.372 Ligands: BEF.23, MG.24 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.258, D:T.259, D:T.259, D:G.260, D:T.262, D:T.262, D:L.263, E:R.372 Salt bridges: E:R.369, E:R.369 ADP.25: 15 residues within 4Å: Chain E: 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, L.698 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.490, E:G.490, E:G.531, E:T.532, E:G.533, E:K.534, E:T.535, E:Q.670 Salt bridges: E:K.534 ADP.26: 14 residues within 4Å: Chain E: D.215, I.216, G.217, G.258, T.259, G.260, K.261, T.262, L.263, V.390, I.393, H.394, G.418, A.419 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.217, E:G.217, E:G.258, E:T.259, E:G.260, E:K.261, E:T.262, E:L.263

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

BEF.2: 9 residues within 4Å: Chain A: P.530, G.531, K.534, T.535, N.634 Chain B: R.645, R.648 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 8 residues within 4Å: Chain A: P.256, P.257, G.258, T.259, K.261 Chain B: R.369 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) BEF.10: 10 residues within 4Å: Chain B: P.256, P.257, G.258, K.261, T.262, N.358 Chain C: R.369, R.372 Ligands: ADP.9, MG.11 No protein-ligand interaction detected (PLIP) BEF.12: 9 residues within 4Å: Chain B: P.530, G.531, K.534, E.588, N.634 Chain C: R.645, R.648 Ligands: ADP.7, MG.8 No protein-ligand interaction detected (PLIP) BEF.14: 8 residues within 4Å: Chain C: P.530, G.531, K.534, T.535 Chain D: R.645, R.648 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP) BEF.17: 9 residues within 4Å: Chain C: P.257, G.258, K.261, T.262, N.358 Chain D: R.369, R.372 Ligands: ADP.16, MG.18 No protein-ligand interaction detected (PLIP) BEF.20: 5 residues within 4Å: Chain D: P.530, T.535 Chain E: R.648 Ligands: ADP.19, MG.21 No protein-ligand interaction detected (PLIP) BEF.23: 7 residues within 4Å: Chain D: P.256, P.257, G.258, K.261, N.358 Ligands: ADP.22, MG.24 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.535, D.587 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.535 MG.6: 3 residues within 4Å: Chain A: T.262 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.262 MG.8: 4 residues within 4Å: Chain B: T.535, D.587 Ligands: ADP.7, BEF.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.535 MG.11: 4 residues within 4Å: Chain B: T.262, D.314 Ligands: ADP.9, BEF.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.262 MG.15: 4 residues within 4Å: Chain C: T.535, D.587 Ligands: ADP.13, BEF.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.535 MG.18: 4 residues within 4Å: Chain C: T.262, D.314 Ligands: ADP.16, BEF.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.262 MG.21: 3 residues within 4Å: Chain D: T.535 Ligands: ADP.19, BEF.20 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.535 MG.24: 4 residues within 4Å: Chain D: T.262, D.314 Ligands: ADP.22, BEF.23 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cooney, I. et al., Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Science (2019)

Release Date

2019-07-10

Peptides

Cell division control protein 48: ABCDEF
Substrate bound to the central pore of the Cdc48 hexamer: G
UBX domain-containing protein 1: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
Z

Cell division control protein 48

Substrate bound to the central pore of the Cdc48 hexamer

UBX domain-containing protein 1

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