SMTL ID : 7psm.1

S. cerevisiae Atm1 in MSP1D1 nanodiscs with bound AMP-PNP and Mg2+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

ANP.1: 20 residues within 4Å: Chain A: Y.354, H.355, R.358, I.360, S.380, G.381, G.383, K.384, S.385, T.386, Q.426, H.540 Chain B: L.463, M.481, I.482, S.483, G.484, G.485, A.511 Ligands: MG.2 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:S.483, B:S.483, B:G.484, B:G.485, B:A.511, A:R.358, A:R.358, A:G.381, A:G.383, A:K.384, A:K.384, A:S.385, A:T.386, A:Q.426 pi-Stacking: A:Y.354, A:Y.354 ANP.4: 20 residues within 4Å: Chain A: L.463, M.481, I.482, S.483, G.484, G.485, A.511 Chain B: Y.354, H.355, R.358, I.360, S.380, G.381, G.383, K.384, S.385, T.386, Q.426, H.540 Ligands: MG.5 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.358, B:R.358, B:G.381, B:G.383, B:K.384, B:K.384, B:S.385, B:T.386, B:Q.426, A:S.483, A:S.483, A:G.484, A:G.485, A:A.511 pi-Stacking: B:Y.354, B:Y.354

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: Q.426 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: S.385, Q.426 Ligands: ANP.4 No protein-ligand interaction detected (PLIP)

2 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.3: 10 residues within 4Å: Chain A: V.35, Q.36, F.39, F.150, S.153, V.154, G.157, I.158, Y.161, Q.162 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.35, A:F.150, A:F.150, A:Y.161 Hydrogen bonds: A:Q.36, A:Q.162 LOP.6: 10 residues within 4Å: Chain B: V.35, Q.36, F.39, F.150, S.153, V.154, G.157, I.158, Y.161, Q.162 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.35, B:F.150, B:F.150, B:Y.161 Hydrogen bonds: B:Q.36, B:Q.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ellinghaus, T.L. et al., Conformational changes in the yeast mitochondrial ABC transporter Atm1 during the transport cycle. Sci Adv (2021)

Release Date

2021-12-29

Peptides

Iron-sulfur clusters transporter ATM1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Iron-sulfur clusters transporter ATM1, mitochondrial

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