SMTL ID : 9m3w.1

Arabidopsis thaliana CDC48A bound to AMP-PNP (AMPPNP-Up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

homo-hexamer

Ligands

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

ANP.1: 22 residues within 4Å: Chain A: D.486, I.487, G.488, L.490, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, A.668, G.693, A.694, T.697 Chain B: R.644, P.645, R.775 Ligands: MG.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.488, A:G.529, A:C.530, A:G.531, A:K.532, A:K.532, A:T.533, A:T.533, A:L.534, A:D.585, A:N.633, B:R.644, B:R.775, B:R.775 ANP.3: 21 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, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Chain B: R.367, F.368 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.215, 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:N.356, A:H.392 ANP.5: 22 residues within 4Å: Chain B: D.486, I.487, G.488, L.490, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, A.668, G.693, A.694, T.697 Chain C: R.644, P.645, R.775 Ligands: MG.6 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.488, B:G.529, B:C.530, B:G.531, B:K.532, B:K.532, B:T.533, B:T.533, B:L.534, B:D.585, B:N.633, C:R.644, C:R.775, C:R.775 ANP.7: 21 residues within 4Å: Chain B: D.213, V.214, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Chain C: R.367, F.368 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain B 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:L.261, B:E.313, B:N.356, B:H.392 ANP.9: 22 residues within 4Å: Chain C: D.486, I.487, G.488, L.490, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, A.668, G.693, A.694, T.697 Chain D: R.644, P.645, R.775 Ligands: MG.10 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.488, C:G.529, C:C.530, C:G.531, C:K.532, C:K.532, C:T.533, C:T.533, C:L.534, C:D.585, C:N.633, D:R.644, D:R.775, D:R.775 ANP.11: 21 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, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Chain D: R.367, F.368 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.215, C:G.215, C:G.256, C:S.257, C:G.258, C:K.259, C:K.259, C:T.260, C:L.261, C:E.313, C:N.356, C:H.392 ANP.13: 22 residues within 4Å: Chain D: D.486, I.487, G.488, L.490, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, A.668, G.693, A.694, T.697 Chain E: R.644, P.645, R.775 Ligands: MG.14 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.488, D:G.529, D:C.530, D:G.531, D:K.532, D:K.532, D:T.533, D:T.533, D:L.534, D:D.585, D:N.633, E:R.644, E:R.775, E:R.775 ANP.15: 21 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, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Chain E: R.367, F.368 Ligands: MG.16 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.215, D:G.215, D:G.256, D:S.257, D:G.258, D:K.259, D:K.259, D:T.260, D:L.261, D:E.313, D:N.356, D:H.392 ANP.17: 22 residues within 4Å: Chain E: D.486, I.487, G.488, L.490, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, A.668, G.693, A.694, T.697 Chain F: R.644, P.645, R.775 Ligands: MG.18 14 PLIP interactions: 3 interactions with chain F, 11 interactions with chain E Hydrogen bonds: F:R.644, F:R.775, F:R.775, E:G.488, E:G.529, E:C.530, E:G.531, E:K.532, E:K.532, E:T.533, E:T.533, E:L.534, E:D.585, E:N.633 ANP.19: 21 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, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Chain F: R.367, F.368 Ligands: MG.20 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.215, E:G.215, E:G.256, E:S.257, E:G.258, E:K.259, E:K.259, E:T.260, E:L.261, E:E.313, E:N.356, E:H.392 ANP.21: 22 residues within 4Å: Chain A: R.644, P.645, R.775 Chain F: D.486, I.487, G.488, L.490, P.528, G.529, C.530, G.531, K.532, T.533, L.534, D.585, N.633, I.665, A.668, G.693, A.694, T.697 Ligands: MG.22 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain F Hydrogen bonds: A:R.644, A:R.775, A:R.775, F:G.488, F:G.529, F:C.530, F:G.531, F:K.532, F:K.532, F:T.533, F:T.533, F:L.534, F:D.585, F:N.633 ANP.23: 21 residues within 4Å: Chain A: R.367, F.368 Chain F: D.213, V.214, G.215, P.255, G.256, S.257, G.258, K.259, T.260, L.261, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Ligands: MG.24 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.215, F:G.215, F:G.256, F:S.257, F:G.258, F:K.259, F:K.259, F:T.260, F:L.261, F:E.313, F:N.356, F:H.392

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.532, T.533, D.585, E.586, A.631, N.633 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.585 MG.4: 5 residues within 4Å: Chain A: K.259, T.260, D.312, E.313 Ligands: ANP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.260, A:D.312, A:D.312 MG.6: 7 residues within 4Å: Chain B: K.532, T.533, D.585, E.586, A.631, N.633 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.585 MG.8: 5 residues within 4Å: Chain B: K.259, T.260, D.312, E.313 Ligands: ANP.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.260, B:D.312, B:D.312 MG.10: 7 residues within 4Å: Chain C: K.532, T.533, D.585, E.586, A.631, N.633 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.585 MG.12: 5 residues within 4Å: Chain C: K.259, T.260, D.312, E.313 Ligands: ANP.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.260, C:D.312, C:D.312 MG.14: 7 residues within 4Å: Chain D: K.532, T.533, D.585, E.586, A.631, N.633 Ligands: ANP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.585 MG.16: 5 residues within 4Å: Chain D: K.259, T.260, D.312, E.313 Ligands: ANP.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.260, D:D.312, D:D.312 MG.18: 7 residues within 4Å: Chain E: K.532, T.533, D.585, E.586, A.631, N.633 Ligands: ANP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.585 MG.20: 5 residues within 4Å: Chain E: K.259, T.260, D.312, E.313 Ligands: ANP.19 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.260, E:D.312, E:D.312 MG.22: 7 residues within 4Å: Chain F: K.532, T.533, D.585, E.586, A.631, N.633 Ligands: ANP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.585 MG.24: 5 residues within 4Å: Chain F: K.259, T.260, D.312, E.313 Ligands: ANP.23 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.260, F:D.312, F:D.312

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Cell division control protein 48 homolog A

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