SMTL ID : 9m3z.1

Arabidopsis thaliana CDC48A-NPL4-UFD1B (AtCNU) complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-6-1-mer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: D.213, V.214, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, E.313, H.392, G.416, A.417 Chain B: R.367 Ligands: MG.2 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.215, A:G.256, A:S.257, A:G.258, A:K.259, A:K.259, A:T.260, A:L.261, A:E.313, A:E.313, B:R.367 Salt bridges: B:R.367 ANP.4: 16 residues within 4Å: Chain B: D.213, V.214, G.215, G.256, S.257, G.258, K.259, T.260, L.261, D.312, H.392, G.416, A.417 Chain C: R.367, F.368 Ligands: MG.5 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.215, B:G.215, B:G.256, B:S.257, B:G.258, B:K.259, B:K.259, B:T.260, B:T.260, B:L.261, C:R.367, C:R.367 ANP.7: 17 residues within 4Å: Chain C: D.213, V.214, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, E.313, H.392, G.416, A.417 Chain D: R.367, F.368 Ligands: MG.8 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.215, C:G.256, C:S.257, C:S.257, C:G.258, C:K.259, C:K.259, C:K.259, C:T.260, C:L.261, C:E.313, D:R.367 ANP.10: 17 residues within 4Å: Chain D: D.213, V.214, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, N.356, V.388, H.392, G.416, A.417 Chain E: R.367 Ligands: MG.11 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.215, D:G.215, D:G.256, D:G.258, D:K.259, D:K.259, D:T.260, D:L.261, E:R.367 ANP.13: 17 residues within 4Å: Chain E: D.213, V.214, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, V.388, H.392, G.416, A.417 Chain F: R.367, F.368 Ligands: MG.14 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.215, E:G.256, E:S.257, E:G.258, E:K.259, E:K.259, E:K.259, E:K.259, E:T.260, E:T.260, F:R.367 ANP.16: 17 residues within 4Å: Chain A: R.367, F.368 Chain F: D.213, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, D.312, V.388, H.392, G.416, A.417 Ligands: MG.17 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.215, F:G.215, F:G.256, F:S.257, F:G.258, F:K.259, F:K.259, F:K.259, F:T.260, F:L.261, A:R.367

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.259, T.260 Chain B: R.367 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.260 MG.5: 3 residues within 4Å: Chain B: T.260, D.312 Ligands: ANP.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.260, B:D.312, B:D.312 MG.8: 2 residues within 4Å: Chain C: T.260 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.260 MG.11: 3 residues within 4Å: Chain D: K.259, T.260 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain E: T.260, D.312 Ligands: ANP.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.260, E:D.312, E:D.312 MG.17: 3 residues within 4Å: Chain F: T.260, D.312 Ligands: ANP.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.260, F:D.312

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

ADP.3: 11 residues within 4Å: Chain A: I.487, P.528, G.529, C.530, G.531, K.532, T.533, L.534, I.665, G.693 Chain B: R.644 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Salt bridges: B:R.644, A:K.532, A:K.532 Hydrogen bonds: A:G.529, A:G.531, A:K.532, A:T.533, A:T.533, A:L.534 ADP.6: 13 residues within 4Å: Chain B: D.486, I.487, G.529, C.530, G.531, K.532, T.533, L.534, I.665, G.693, A.694, T.697 Chain C: R.644 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.487, B:G.529, B:C.530, B:G.531, B:K.532 Salt bridges: B:K.532, B:K.532, C:R.644 ADP.9: 15 residues within 4Å: Chain C: D.486, I.487, G.488, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, T.697 Chain D: R.644 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.488, C:G.488, C:G.529, C:C.530, C:G.531, C:K.532, C:T.533, C:T.533, C:T.533, C:D.585, C:N.633, C:T.697 Salt bridges: C:K.532, C:K.532, D:R.644 ADP.12: 14 residues within 4Å: Chain D: D.486, I.487, P.528, G.529, C.530, G.531, K.532, T.533, L.534, I.665, G.693, A.694, T.697 Chain E: R.644 10 PLIP interactions: 1 interactions with chain E, 9 interactions with chain D Hydrogen bonds: E:R.644, D:I.487, D:G.529, D:C.530, D:G.531, D:K.532, D:T.533, D:T.697 Salt bridges: D:K.532, D:K.532 ADP.15: 14 residues within 4Å: Chain E: D.486, I.487, G.488, P.528, G.529, C.530, G.531, K.532, T.533, L.534, I.665, G.693, T.697 Chain F: R.644 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.488, E:G.488, E:G.529, E:C.530, E:G.531, E:K.532, E:T.533, E:T.533, E:T.697 Salt bridges: E:K.532, E:K.532, F:R.644 ADP.18: 14 residues within 4Å: Chain A: R.644 Chain F: D.486, I.487, G.488, P.528, G.529, C.530, G.531, K.532, T.533, L.534, I.665, G.693, T.697 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.488, F:G.488, F:G.529, F:C.530, F:G.531, F:K.532, F:T.533, F:T.533, F:T.697 Salt bridges: F:K.532, F:K.532, A:R.644

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huntington, B. et al., Plant-specific adaptations of the CDC48 unfoldase. To Be Published

Release Date

2025-10-29

Peptides

Cell division control protein 48 homolog A: ABCDEF
NPL4-like protein 2: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Cell division control protein 48 homolog A

NPL4-like protein 2

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