SMTL ID : 7njm.1

Mycobacterium smegmatis ATP synthase state 1c

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-9-1-1-1-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: D.173, R.174, K.175, T.176, G.177, K.178, T.179, A.180, E.331, F.360, R.365, P.366, Q.433, P.434, Q.435 Chain D: Y.366 Ligands: MG.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.175, A:T.176, A:T.176, A:G.177, A:K.178, A:T.179, A:A.180, A:Q.433, A:Q.435, A:Q.435, A:Q.435, D:Y.366 Water bridges: A:K.178, A:K.178, A:T.179 Salt bridges: A:K.175, A:K.175, A:K.175, A:K.178, A:K.178 pi-Stacking: A:F.360 ATP.3: 17 residues within 4Å: Chain B: D.173, R.174, K.175, T.176, G.177, K.178, T.179, A.180, E.331, F.360, R.365, P.366, Q.433, P.434, Q.435 Chain E: D.357 Ligands: MG.4 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:K.175, B:T.176, B:T.176, B:G.177, B:K.178, B:T.179, B:T.179, B:A.180, B:Q.433, B:Q.435, B:Q.435, B:Q.435, E:D.357 Water bridges: B:T.179, B:T.179, B:D.272 Salt bridges: B:K.175, B:K.178, B:K.178 pi-Stacking: B:F.360 ATP.5: 17 residues within 4Å: Chain C: D.173, R.174, K.175, T.176, G.177, K.178, T.179, A.180, F.360, R.365, P.366, Q.433, P.434, Q.435 Chain F: D.357, Y.366 Ligands: MG.6 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:K.175, C:T.176, C:T.176, C:G.177, C:K.178, C:T.179, C:A.180, C:Q.433, C:Q.435, C:Q.435, C:Q.435, F:Y.366 Water bridges: C:T.179, C:T.179 Salt bridges: C:K.175, C:K.178, C:K.178 pi-Stacking: C:F.360, C:F.360 ATP.10: 22 residues within 4Å: Chain B: I.346, S.347, V.374, R.376 Chain F: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.192, R.193, Y.309, F.338, F.343, M.416, A.419, F.422, T.423 Ligands: MG.11 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain F Hydrogen bonds: B:S.347, F:G.163, F:V.164, F:G.165, F:K.166, F:T.167, F:V.168 Salt bridges: B:R.376, B:R.376, B:R.376, F:K.166, F:K.166, F:R.193 Water bridges: F:T.167, F:R.193, F:R.193, F:R.193 pi-Stacking: F:F.343, F:F.343

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.179, D.272 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.179, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: T.179, D.272 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.179, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain C: T.179 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.179, H2O.1, H2O.1, H2O.1 MG.8: 6 residues within 4Å: Chain C: R.376 Chain D: T.167, E.192, R.193, E.196 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.167, H2O.1, H2O.1, H2O.1, H2O.1 MG.11: 6 residues within 4Å: Chain F: K.166, T.167, E.192, R.193, E.196 Ligands: ATP.10 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.167, H2O.1, H2O.1, H2O.1

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

ADP.7: 23 residues within 4Å: Chain C: V.374, S.375, R.376, L.395 Chain D: A.162, G.163, V.164, G.165, K.166, T.167, V.168, E.196, F.338, F.343, P.344, Q.414, N.415, M.416, A.419, F.422, T.423, L.457 Ligands: MG.8 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.161, D:G.163, D:V.164, D:G.165, D:K.166, D:T.167, D:V.168, D:E.196, C:S.375 Water bridges: D:T.167, D:R.193, D:R.193, C:R.376, C:R.376 Salt bridges: D:K.166, C:R.376, C:R.376 pi-Stacking: D:F.343, D:F.343 ADP.9: 14 residues within 4Å: Chain E: G.161, A.162, G.163, V.164, G.165, K.166, T.167, V.168, F.338, F.343, M.416, A.419, F.422, T.423 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.161, E:G.163, E:V.164, E:G.165, E:K.166, E:T.167, E:T.167, E:T.167, E:V.168 pi-Stacking: E:F.343, E:F.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montgomery, M.G. et al., Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-10-27

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit c: IJKLMNOPQ
ATP synthase subunit a: R
ATP synthase subunit b: S
ATP synthase subunit b-delta: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
L

J
M

K
N

L
O

M
P

N
Q

O
R

P
S

Q
T

R
a

S
b

T
d

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit c

ATP synthase subunit a

ATP synthase subunit b

ATP synthase subunit b-delta

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