SMTL ID : 3zk1.2 (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: 3 interactions with chain A Hydrogen bonds: A:S.66, A:S.66, A:T.67 NA.6: 5 residues within 4Å: Chain B: V.63, A.64, S.66 Chain C: E.32, E.65 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.66, B:T.67, C:E.65 NA.8: 5 residues within 4Å: Chain C: V.63, A.64, S.66 Chain D: E.32, E.65 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.32, C:S.66, C:T.67 NA.10: 5 residues within 4Å: Chain D: V.63, A.64, S.66 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.12: 6 residues within 4Å: Chain E: V.63, A.64, S.66, T.67 Chain F: E.32, E.65 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.66, E:T.67, F:E.32 NA.14: 6 residues within 4Å: Chain F: V.63, A.64, S.66, T.67 Chain G: E.32, E.65 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:E.32, F:S.66, F:T.67 NA.17: 5 residues within 4Å: Chain G: V.63, A.64, S.66 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.19: 5 residues within 4Å: Chain H: V.63, A.64, S.66 Chain I: E.32, E.65 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.66, H:S.66, H:T.67 NA.21: 4 residues within 4Å: Chain I: V.63, S.66 Chain J: E.32, E.65 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:S.66, J:E.32 NA.23: 6 residues within 4Å: Chain J: V.63, A.64, S.66, T.67 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: SUGAR (DECYL-BETA-D-MALTOPYRANOSIDE)(Non-covalent)

DMU.2: 6 residues within 4Å: Chain A: I.9, C.13 Chain K: I.9, C.13 Ligands: DMU.4, DMU.24 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain K Hydrophobic interactions: A:I.9, A:I.9, K:I.9 DMU.4: 9 residues within 4Å: Chain A: M.1, T.5, C.13 Chain B: D.2, I.9, C.13, V.16 Ligands: DMU.2, DMU.7 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.1 Hydrophobic interactions: B:I.9, B:I.9, B:V.16 DMU.7: 10 residues within 4Å: Chain B: M.1, I.9, C.13 Chain C: M.1, D.2, T.5, I.9, V.16 Ligands: DMU.4, DMU.9 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.9, C:I.9, C:V.16, B:I.9, B:I.9 Hydrogen bonds: C:D.2, C:D.2, C:T.5, B:M.1 Water bridges: B:T.5 DMU.9: 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.11 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.9 Hydrogen bonds: D:T.5, C:M.1, C:M.1 DMU.11: 8 residues within 4Å: Chain D: M.1, I.9, C.13 Chain E: T.5, I.9, C.13 Ligands: DMU.9, DMU.13 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:I.9, E:I.9, E:I.9 Hydrogen bonds: D:M.1, D:M.1, E:T.5, E:T.5 DMU.13: 6 residues within 4Å: Chain E: M.1, I.9, C.13 Chain F: V.16 Ligands: DMU.11, DMU.15 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:I.9, F:V.16 Hydrogen bonds: E:M.1 Water bridges: F:T.5, F:T.5 DMU.15: 8 residues within 4Å: Chain F: M.1, I.9, C.13 Chain G: T.5, I.9, C.13 Ligands: DMU.13, DMU.18 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:T.5, G:I.9, G:I.9, F:I.9, F:I.9 Hydrogen bonds: G:T.5 DMU.18: 7 residues within 4Å: Chain G: M.1, I.9 Chain H: M.1, T.5, I.9 Ligands: DMU.15, DMU.20 7 PLIP interactions: 4 interactions with chain G, 3 interactions with chain H Hydrophobic interactions: G:I.9, G:I.9, H:T.5, H:I.9, H:I.9 Hydrogen bonds: G:M.1, G:M.1 DMU.20: 7 residues within 4Å: Chain H: M.1, I.9, C.13 Chain I: T.5, C.13 Ligands: DMU.18, DMU.22 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:I.9 Hydrogen bonds: H:M.1, H:M.1 DMU.22: 11 residues within 4Å: Chain I: M.1, I.9, C.13 Chain J: M.1, D.2, T.5, I.9, C.13, V.16 Ligands: DMU.20, DMU.24 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:I.9, J:V.16, I:I.9 Hydrogen bonds: J:D.2, J:D.2, I:M.1 DMU.24: 4 residues within 4Å: Chain J: C.13 Chain K: T.5 Ligands: DMU.2, DMU.22 No protein-ligand interaction detected (PLIP)

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.5: 2 residues within 4Å: Chain B: K.87 Chain C: Y.80 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.87, C:Y.80, C:Y.80 Water bridges: C:N.82 TAM.16: 3 residues within 4Å: Chain F: S.55, L.59 Chain G: R.50 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.50

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
L

B
M

C
N

D
O

E
P

F
Q

G
R

H
S

I
T

J
U

K
V

Membrane

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

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