SMTL ID : 7md2.1

The F1 region of ammocidin-bound Saccharomyces cerevisiae ATP synthase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, N.433, Q.434 Chain D: R.356, D.359, Y.368 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.174, A:T.175, A:G.176, A:G.176, A:K.177, A:T.178, A:A.179, A:R.364, A:Q.432, A:Q.434, A:Q.434 Salt bridges: A:K.177, A:K.177 ATP.3: 15 residues within 4Å: Chain B: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, N.433, Q.434 Chain E: R.356 Ligands: MG.4 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:Q.174, B:T.175, B:G.176, B:K.177, B:T.178, B:A.179, B:R.364, B:Q.432, B:Q.434, B:Q.434 Salt bridges: B:K.177, B:K.177, E:R.356, E:R.356, E:R.356 ATP.5: 17 residues within 4Å: Chain C: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, N.433, Q.434 Chain F: K.354, R.356, Y.368 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.174, C:T.175, C:T.175, C:G.176, C:K.177, C:T.178, C:T.178, C:A.179, C:Q.432, C:Q.434, C:Q.434 Salt bridges: C:K.177, C:K.177

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.177, T.178, D.271 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.178 MG.4: 5 residues within 4Å: Chain B: K.177, T.178, D.271 Chain E: R.356 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.178 MG.6: 3 residues within 4Å: Chain C: T.178, D.271 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.178

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain B: S.346 Chain F: A.159, G.160, V.161, G.162, K.163, T.164, R.190 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.160, F:V.161, F:G.162, F:K.163, F:T.164 Salt bridges: F:K.163, F:R.190

1 x ZHD: (3~{E},5~{Z},7~{E},9~{R},10~{S},11~{E},13~{E},15~{E},17~{R},18~{S},20~{S})-20-[(1~{R})-1-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-[(2~{S},4~{S},5~{S},6~{R})-5-[(2~{S},4~{R},5~{R},6~{R})-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-methyl-4-oxidanyl-oxan-2-yl]oxy-3-methoxy-6-(3-methoxypropyl)-5-methyl-2,4-bis(oxidanyl)oxan-2-yl]ethyl]-5,18-dimethoxy-3,7,9,11,13,15-hexamethyl-10-[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-17-oxidanyl-1-oxacycloicosa-3,5,7,11,13,15-hexaen-2-one(Non-covalent)

ZHD.8: 31 residues within 4Å: Chain A: Q.407, F.408 Chain C: A.404, F.405, F.408, D.411, L.412 Chain D: L.384, D.386, I.387, I.390, L.391, E.395, L.396, S.397, D.400 Chain F: D.386, I.387, I.390, L.391 Chain G: N.15, I.16, I.19, T.22, M.23, V.26, R.30, K.81, G.82, L.83, R.233 25 PLIP interactions: 9 interactions with chain D, 10 interactions with chain G, 5 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: D:L.384, D:I.387, D:I.390, D:I.390, D:I.390, D:L.396, G:I.16, G:I.16, G:V.26, G:K.81, C:F.405, C:F.405, C:F.408, C:F.408, C:L.412, F:I.387 Hydrogen bonds: D:S.397, D:D.400, D:D.400, G:R.30, G:R.30, G:K.81, G:G.82 Salt bridges: G:R.30, G:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reisman, B.J. et al., A Family of Glycosylated Macrolides Selectively Target Energetic Vulnerabilities in Leukemia. Biorxiv (2021)

Release Date

2021-08-11

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase subunit gamma: G
ATP synthase subunit epsilon, mitochondrial: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase subunit gamma

ATP synthase subunit epsilon, mitochondrial

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