SMTL ID : 9m3x.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

homo-hexamer

Ligands

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

ANP.1: 23 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, E.586, N.633, I.665, A.668, G.693, A.694, T.697 Chain F: R.644, P.645, R.775 Ligands: MG.3 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:G.488, A:G.529, A:C.530, A:C.530, A:G.531, A:K.532, A:T.533, A:T.533, A:L.534, A:D.585, A:N.633, A:T.697, F:R.644, F:R.775 ANP.2: 24 residues within 4Å: Chain A: D.213, V.214, G.215, V.217, P.255, G.256, S.257, G.258, K.259, T.260, L.261, R.264, D.312, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Chain F: R.367, F.368 Ligands: MG.4 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.215, A:G.256, A:S.257, A:S.257, A:G.258, A:K.259, A:T.260, A:R.264, A:D.312, A:E.313, A:H.392, F:R.367 ANP.5: 23 residues within 4Å: Chain A: R.644, P.645, R.775 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, E.586, N.633, I.665, A.668, G.693, A.694, T.697 Ligands: MG.7 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.488, B:G.529, B:C.530, B:C.530, B:G.531, B:K.532, B:T.533, B:T.533, B:L.534, B:D.585, B:N.633, B:T.697, A:R.644, A:R.775 ANP.6: 24 residues within 4Å: Chain A: R.367, F.368 Chain B: D.213, V.214, G.215, V.217, P.255, G.256, S.257, G.258, K.259, T.260, L.261, R.264, D.312, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Ligands: MG.8 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.367, B:G.215, B:G.256, B:S.257, B:S.257, B:G.258, B:K.259, B:T.260, B:R.264, B:D.312, B:E.313, B:H.392 ANP.9: 23 residues within 4Å: Chain B: R.644, P.645, R.775 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, E.586, N.633, I.665, A.668, G.693, A.694, T.697 Ligands: MG.11 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.488, C:G.529, C:C.530, C:C.530, C:G.531, C:K.532, C:T.533, C:T.533, C:L.534, C:D.585, C:N.633, C:T.697, B:R.644, B:R.775 ANP.10: 24 residues within 4Å: Chain B: R.367, F.368 Chain C: D.213, V.214, G.215, V.217, P.255, G.256, S.257, G.258, K.259, T.260, L.261, R.264, D.312, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Ligands: MG.12 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.215, C:G.256, C:S.257, C:S.257, C:G.258, C:K.259, C:T.260, C:R.264, C:D.312, C:E.313, C:H.392, B:R.367 ANP.13: 23 residues within 4Å: Chain C: R.644, P.645, R.775 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, E.586, N.633, I.665, A.668, G.693, A.694, T.697 Ligands: MG.15 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.488, D:G.529, D:C.530, D:C.530, D:G.531, D:K.532, D:T.533, D:T.533, D:L.534, D:D.585, D:N.633, D:T.697, C:R.644, C:R.775 ANP.14: 24 residues within 4Å: Chain C: R.367, F.368 Chain D: D.213, V.214, G.215, V.217, P.255, G.256, S.257, G.258, K.259, T.260, L.261, R.264, D.312, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Ligands: MG.16 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.215, D:G.256, D:S.257, D:S.257, D:G.258, D:K.259, D:T.260, D:R.264, D:D.312, D:E.313, D:H.392, C:R.367 ANP.17: 23 residues within 4Å: Chain D: R.644, P.645, R.775 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, E.586, N.633, I.665, A.668, G.693, A.694, T.697 Ligands: MG.19 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.488, E:G.529, E:C.530, E:C.530, E:G.531, E:K.532, E:T.533, E:T.533, E:L.534, E:D.585, E:N.633, E:T.697, D:R.644, D:R.775 ANP.18: 24 residues within 4Å: Chain D: R.367, F.368 Chain E: D.213, V.214, G.215, V.217, P.255, G.256, S.257, G.258, K.259, T.260, L.261, R.264, D.312, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Ligands: MG.20 12 PLIP interactions: 11 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.215, E:G.256, E:S.257, E:S.257, E:G.258, E:K.259, E:T.260, E:R.264, E:D.312, E:E.313, E:H.392, D:R.367 ANP.21: 23 residues within 4Å: Chain E: 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, E.586, N.633, I.665, A.668, G.693, A.694, T.697 Ligands: MG.23 14 PLIP interactions: 2 interactions with chain E, 12 interactions with chain F Hydrogen bonds: E:R.644, E:R.775, F:G.488, F:G.529, F:C.530, F:C.530, F:G.531, F:K.532, F:T.533, F:T.533, F:L.534, F:D.585, F:N.633, F:T.697 ANP.22: 24 residues within 4Å: Chain E: R.367, F.368 Chain F: D.213, V.214, G.215, V.217, P.255, G.256, S.257, G.258, K.259, T.260, L.261, R.264, D.312, E.313, N.356, V.388, I.391, H.392, G.416, A.417, A.420 Ligands: MG.24 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.215, F:G.256, F:S.257, F:S.257, F:G.258, F:K.259, F:T.260, F:R.264, F:D.312, F:E.313, F:H.392, E:R.367

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: K.532, 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: 4 residues within 4Å: Chain A: T.260, D.312, E.313 Ligands: ANP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.260, A:D.312 MG.7: 7 residues within 4Å: Chain A: R.644 Chain B: K.532, 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: 4 residues within 4Å: Chain B: T.260, D.312, E.313 Ligands: ANP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.260, B:D.312 MG.11: 6 residues within 4Å: Chain C: K.532, 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: 4 residues within 4Å: Chain C: T.260, D.312, E.313 Ligands: ANP.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.260, C:D.312 MG.15: 6 residues within 4Å: Chain D: K.532, 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: 4 residues within 4Å: Chain D: T.260, D.312, E.313 Ligands: ANP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.260, D:D.312 MG.19: 6 residues within 4Å: Chain E: K.532, 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: 4 residues within 4Å: Chain E: T.260, D.312, E.313 Ligands: ANP.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.260, E:D.312 MG.23: 6 residues within 4Å: Chain F: K.532, 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: 4 residues within 4Å: Chain F: T.260, D.312, E.313 Ligands: ANP.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.260, 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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