SMTL ID : 7ttr.1

Skd3_ATPyS_FITC-casein Hexamer, AAA+ only

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: H.223, I.224, I.225, S.260, G.261, I.262, G.263, K.264, T.265, E.266, D.331, F.448, A.496, R.497 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.223, A:I.225, A:G.261, A:G.261, A:G.263, A:K.264, A:T.265, A:E.266, A:R.497 Salt bridges: A:R.497

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.265, D.331 Ligands: AGS.3 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain B: R.438 Chain C: T.265, D.331, E.332 Ligands: AGS.5 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: T.265, D.331, E.332 Ligands: AGS.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.265, D:E.332 MG.9: 3 residues within 4Å: Chain E: T.265, D.331 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.265

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.3: 17 residues within 4Å: Chain B: H.223, I.224, I.225, S.260, G.261, I.262, G.263, K.264, T.265, E.266, E.332, F.448, L.456, A.496, R.497, K.500 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:I.225, B:G.261, B:I.262, B:I.262, B:G.263, B:G.263, B:K.264, B:T.265, B:E.266, B:E.266, B:R.497, B:R.497 Salt bridges: B:K.264, B:R.497, B:R.497 AGS.5: 20 residues within 4Å: Chain B: H.250, E.434, R.438 Chain C: H.223, I.224, I.225, S.260, G.261, I.262, G.263, K.264, T.265, E.266, E.332, F.448, L.456, K.459, A.496, R.497 Ligands: MG.4 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.225, C:I.225, C:G.261, C:I.262, C:G.263, C:K.264, C:K.264, C:T.265, C:T.265, C:T.265, C:E.266, C:E.266, C:R.497, B:R.438, B:R.438 Salt bridges: C:K.264, C:R.497 AGS.6: 20 residues within 4Å: Chain C: E.434, R.438 Chain D: H.223, I.224, I.225, S.259, S.260, G.261, I.262, G.263, K.264, T.265, E.332, N.373, F.448, L.456, A.496, R.497, K.500 Ligands: MG.7 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:H.223, D:I.225, D:G.261, D:I.262, D:G.263, D:K.264, D:K.264, D:T.265, D:T.265, D:R.497, D:K.500, C:R.438, C:R.438 Salt bridges: D:K.264, D:K.264, D:R.497, D:R.497, C:R.438 AGS.8: 22 residues within 4Å: Chain D: H.250, E.434, R.438 Chain E: H.223, I.224, I.225, S.259, S.260, G.261, I.262, G.263, K.264, T.265, E.266, E.332, N.373, F.448, L.456, K.459, A.496, R.497 Ligands: MG.9 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:I.225, E:G.261, E:I.262, E:I.262, E:G.263, E:K.264, E:T.265, E:T.265, E:E.266, E:E.266, E:K.459, E:R.497, D:R.438, D:R.438 Salt bridges: E:K.264, E:R.497

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cupo, R.R. et al., Unique structural features govern the activity of a human mitochondrial AAA+ disaggregase, Skd3. Cell Rep (2022)

Release Date

2022-09-28

Peptides

Caseinolytic peptidase B protein homolog: ABCDEF
Beta-casein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
P

Caseinolytic peptidase B protein homolog

Beta-casein

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