SMTL ID : 8ub4.1

Cdc48-Shp1 unfolding native substrate, consensus structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-3-mer

Ligands

8 x 08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium(Non-covalent)

08T.1: 22 residues within 4Å: Chain A: D.215, I.216, G.217, C.219, P.257, G.258, T.259, G.260, K.261, T.262, L.263, N.358, V.390, I.393, H.394, G.418, A.419, A.422 Chain B: R.369, F.370, R.372 Ligands: MG.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.217, A:G.258, A:T.259, A:G.260, A:K.261, A:T.262, A:L.263, A:H.394 Salt bridges: A:K.261, B:R.369, B:R.369 08T.3: 22 residues within 4Å: Chain A: D.488, V.489, G.490, L.492, P.530, G.531, T.532, G.533, K.534, T.535, L.536, N.634, I.666, A.669, Q.670, G.694, A.695, L.698 Chain B: D.619, R.645, R.648 Ligands: MG.4 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:T.532, A:G.533, A:K.534, A:T.535, A:L.536, A:Q.670 Salt bridges: A:K.534, B:R.645, B:R.645 08T.5: 24 residues within 4Å: Chain B: D.215, I.216, G.217, C.219, P.257, G.258, T.259, G.260, K.261, T.262, L.263, R.266, N.358, V.390, I.393, H.394, G.418, A.419, A.422 Chain C: D.343, R.369, F.370, R.372 Ligands: MG.6 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.217, B:G.217, B:G.258, B:T.259, B:G.260, B:K.261, B:T.262, B:L.263, B:R.266, C:D.343 Salt bridges: B:K.261, C:R.369, C:R.369 08T.7: 24 residues within 4Å: Chain B: D.488, V.489, G.490, L.492, P.530, G.531, T.532, G.533, K.534, T.535, L.536, K.539, N.634, P.658, I.666, A.669, Q.670, G.694, A.695, L.698 Chain C: D.619, R.645, R.648 Ligands: MG.8 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:T.532, B:G.533, B:K.534, B:T.535, B:L.536, B:Q.670 Salt bridges: B:K.534, C:R.645, C:R.645 08T.9: 26 residues within 4Å: Chain C: D.215, I.216, G.217, G.218, P.257, G.258, T.259, G.260, K.261, T.262, L.263, R.266, N.358, P.382, V.390, I.393, H.394, G.418, A.419, A.422 Chain D: D.343, A.366, R.369, F.370, R.372 Ligands: MG.10 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.258, C:T.259, C:T.259, C:G.260, C:K.261, C:T.262, C:L.263, C:H.394 Salt bridges: C:K.261, D:R.369, D:R.369 08T.11: 23 residues within 4Å: Chain C: D.488, V.489, G.490, L.492, P.530, G.531, T.532, G.533, K.534, T.535, L.536, N.634, P.658, I.666, A.669, Q.670, G.694, A.695, L.698 Chain D: D.619, R.645, R.648 Ligands: MG.12 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain C Salt bridges: D:R.645, D:R.645, C:K.534 Hydrogen bonds: C:G.490, C:G.490, C:G.531, C:T.532, C:T.532, C:G.533, C:K.534, C:T.535, C:L.536, C:Q.670 08T.13: 25 residues within 4Å: Chain D: D.215, I.216, G.217, G.218, C.219, P.257, G.258, T.259, G.260, K.261, T.262, L.263, R.266, N.358, P.382, V.390, I.393, H.394, G.418, A.419, A.422 Chain E: R.369, F.370, R.372 Ligands: MG.14 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain E Hydrogen bonds: 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, E:R.369, E:R.369 08T.15: 23 residues within 4Å: Chain D: D.488, V.489, G.490, L.492, P.530, G.531, T.532, G.533, K.534, T.535, L.536, N.634, P.658, I.666, A.669, Q.670, G.694, A.695, L.698 Chain E: D.619, R.645, R.648 Ligands: MG.16 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.490, D:G.531, D:T.532, 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

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.261, T.262 Chain B: D.343 Ligands: 08T.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.262 MG.4: 3 residues within 4Å: Chain A: T.535 Chain B: R.648 Ligands: 08T.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.535 MG.6: 5 residues within 4Å: Chain B: T.262, D.314 Chain C: G.344, R.372 Ligands: 08T.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.262 MG.8: 2 residues within 4Å: Chain B: T.535 Ligands: 08T.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.535 MG.10: 3 residues within 4Å: Chain C: T.262 Chain D: R.372 Ligands: 08T.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.262 MG.12: 2 residues within 4Å: Chain C: T.535 Ligands: 08T.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.535 MG.14: 4 residues within 4Å: Chain D: K.261, T.262 Chain E: R.372 Ligands: 08T.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.262 MG.16: 2 residues within 4Å: Chain D: T.535 Ligands: 08T.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.535

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

ADP.17: 17 residues within 4Å: Chain E: D.215, I.216, G.217, C.219, P.257, G.258, T.259, G.260, K.261, T.262, L.263, V.390, I.393, H.394, G.418, A.419, A.422 10 PLIP interactions: 10 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:T.262, E:L.263, E:H.394 ADP.18: 16 residues within 4Å: Chain E: D.488, V.489, G.490, G.491, L.492, P.530, G.531, T.532, G.533, K.534, T.535, L.536, I.666, G.694, A.695, L.698 8 PLIP interactions: 8 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:L.536

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cooney, I. et al., Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway. Nat Commun (2024)

Release Date

2024-11-06

Peptides

Cell division control protein 48: ABCDEF
Substrate: G
UBX domain-containing protein 1: HIJ

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

Cell division control protein 48

Substrate

UBX domain-containing protein 1

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