SMTL ID : 3zk1.1 (1 other biounit)

Crystal structure of the sodium binding rotor ring at pH 5.3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-11-mer

Ligands

11 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: E.32, E.65 Chain K: V.63, A.64, S.66 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain A Hydrogen bonds: K:S.66, K:T.67, A:E.65 NA.3: 5 residues within 4Å: Chain A: V.63, A.64, S.66 Chain B: E.32, E.65 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.66, A:T.67, B:E.65 NA.6: 5 residues within 4Å: Chain B: V.63, A.64, S.66 Chain C: E.32, E.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.63, B:S.66, B:T.67 NA.10: 5 residues within 4Å: Chain C: V.63, A.64, S.66 Chain D: E.32, E.65 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.63, C:S.66, C:T.67 NA.12: 6 residues within 4Å: Chain D: V.63, A.64, S.66, T.67 Chain E: E.32, E.65 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:S.66, D:T.67, E:E.32 NA.14: 5 residues within 4Å: Chain E: V.63, A.64, S.66 Chain F: E.32, E.65 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:E.32, E:S.66, E:T.67 NA.16: 6 residues within 4Å: Chain F: V.63, A.64, S.66, T.67 Chain G: E.32, E.65 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:S.66, F:T.67, G:E.32 NA.18: 6 residues within 4Å: Chain G: V.63, A.64, S.66, T.67 Chain H: E.32, E.65 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:S.66, G:T.67, H:E.65 NA.20: 6 residues within 4Å: Chain H: V.63, A.64, S.66, T.67 Chain I: E.32, E.65 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:A.64, H:S.66, H:T.67 NA.22: 6 residues within 4Å: Chain I: V.63, A.64, S.66, T.67 Chain J: E.32, E.65 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:S.66, I:S.66, I:T.67 NA.24: 5 residues within 4Å: Chain J: V.63, A.64, S.66 Chain K: E.32, E.65 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:V.63, J:S.66, J:T.67

11 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.2: 9 residues within 4Å: Chain A: T.5, I.9, C.13, V.16 Chain K: M.1, I.9, C.13 Ligands: DMU.4, DMU.25 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain A Hydrophobic interactions: K:I.9, A:I.9, A:V.16 Hydrogen bonds: K:M.1 DMU.4: 8 residues within 4Å: Chain A: M.1, I.9, C.13 Chain B: T.5, I.9, V.16 Ligands: DMU.2, DMU.7 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.16, A:I.9, A:I.9 Hydrogen bonds: A:M.1, A:M.1 Water bridges: A:D.2 DMU.7: 9 residues within 4Å: Chain B: M.1, I.9, C.13 Chain C: D.2, T.5, I.9, V.16 Ligands: DMU.4, DMU.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.9, C:V.16 Water bridges: B:T.5, C:T.5 DMU.11: 9 residues within 4Å: Chain C: M.1, I.9, C.13 Chain D: D.2, T.5, I.9, C.13 Ligands: DMU.7, DMU.13 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.9, D:I.9 Hydrogen bonds: D:D.2, D:T.5, C:M.1 Water bridges: C:T.5, C:T.5 DMU.13: 9 residues within 4Å: Chain D: M.1, I.9, C.13 Chain E: M.1, D.2, T.5, I.9 Ligands: DMU.11, DMU.15 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:I.9, D:I.9, E:I.9 Hydrogen bonds: D:M.1, E:D.2, E:T.5 DMU.15: 8 residues within 4Å: Chain E: M.1, I.9, C.13 Chain F: T.5, C.13, V.16 Ligands: DMU.13, DMU.17 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.9, F:V.16 Hydrogen bonds: E:M.1, F:T.5 DMU.17: 9 residues within 4Å: Chain F: M.1, T.5, I.9, C.13 Chain G: M.1, D.2, T.5 Ligands: DMU.15, DMU.19 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:I.9 Hydrogen bonds: F:M.1, G:M.1, G:D.2, G:T.5 DMU.19: 10 residues within 4Å: Chain G: M.1, I.9, C.13 Chain H: M.1, D.2, T.5, C.13, V.16 Ligands: DMU.17, DMU.21 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:I.9, H:V.16 Hydrogen bonds: G:M.1, G:M.1, H:M.1, H:D.2 DMU.21: 7 residues within 4Å: Chain H: M.1, I.9, C.13 Chain I: D.2, T.5 Ligands: DMU.19, DMU.23 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:D.2 Hydrophobic interactions: H:I.9 DMU.23: 8 residues within 4Å: Chain I: M.1, I.9 Chain J: M.1, D.2, T.5, I.9 Ligands: DMU.21, DMU.25 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.9, I:I.9 Hydrogen bonds: J:D.2, J:D.2 DMU.25: 6 residues within 4Å: Chain J: M.1, C.13 Chain K: T.5, I.9 Ligands: DMU.2, DMU.23 6 PLIP interactions: 4 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:I.9 Hydrogen bonds: K:M.1, K:M.1, J:M.1, J:M.1 Water bridges: K:D.2

3 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.5: 3 residues within 4Å: Chain A: Y.70, I.77 Chain B: Y.80 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.77 LMT.8: 5 residues within 4Å: Chain B: Y.70, V.73 Chain C: L.76, Y.80 Ligands: LMT.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.70, B:V.73, C:L.76 LMT.9: 5 residues within 4Å: Chain C: I.69, V.73, Y.80, A.81 Ligands: LMT.8 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.69, C:V.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, S. et al., A New Type of Na(+)-Driven ATP Synthase Membrane Rotor with a Two-Carboxylate Ion-Coupling Motif. Plos Biol. (2013)

Release Date

2013-05-29

Peptides

ATP SYNTHASE SUBUNIT C: ABCDEFGHIJK

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
I

J
J

K
K

Membrane

We predict this structure to be a membrane protein.
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ATP SYNTHASE SUBUNIT C

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