SMTL ID : 2wgm.2 (3 other biounits)

Complete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-11-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: Q.32, E.65 Chain K: V.63, A.64, S.66 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain K Hydrogen bonds: A:Q.32, A:Q.32, K:S.66, K:T.67 NA.3: 6 residues within 4Å: Chain A: V.63, A.64, S.66, T.67 Chain B: Q.32, E.65 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.66, A:T.67, B:Q.32, B:Q.32 NA.5: 6 residues within 4Å: Chain B: V.63, A.64, S.66, T.67 Chain C: Q.32, E.65 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.66, B:T.67, C:Q.32, C:Q.32 NA.7: 6 residues within 4Å: Chain C: V.63, A.64, S.66, T.67 Chain D: Q.32, E.65 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.32, C:V.63, C:S.66, C:T.67 NA.9: 5 residues within 4Å: Chain D: V.63, A.64, S.66 Chain E: Q.32, E.65 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:Q.32, D:V.63, D:S.66, D:T.67 NA.11: 6 residues within 4Å: Chain E: V.63, A.64, S.66, T.67 Chain F: Q.32, E.65 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:S.66, E:S.66, E:T.67, F:Q.32 NA.13: 6 residues within 4Å: Chain F: V.63, A.64, S.66, T.67 Chain G: Q.32, E.65 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:Q.32, G:E.65, F:S.66, F:T.67 NA.15: 5 residues within 4Å: Chain G: V.63, S.66, T.67 Chain H: Q.32, E.65 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:Q.32, G:S.66, G:S.66, G:T.67 NA.17: 4 residues within 4Å: Chain H: V.63, S.66 Chain I: Q.32, E.65 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:Q.32, I:Q.32, H:S.66, H:T.67 NA.19: 4 residues within 4Å: Chain I: V.63, S.66 Chain J: Q.32, E.65 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:S.66, I:T.67, J:Q.32, J:E.65 NA.21: 5 residues within 4Å: Chain J: V.63, S.66, T.67 Chain K: Q.32, E.65 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:S.66, J:T.67, K:Q.32, K:E.65

11 x F09: NONAN-1-OL(Non-covalent)

F09.2: 3 residues within 4Å: Chain B: A.12 Ligands: F09.4, F09.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.12 F09.4: 3 residues within 4Å: Chain D: V.16 Ligands: F09.2, F09.6 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.16 F09.6: 4 residues within 4Å: Chain D: A.13 Chain E: V.16 Ligands: F09.4, F09.8 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.16 F09.8: 4 residues within 4Å: Chain E: F.5, A.13 Ligands: F09.6, F09.10 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.13 F09.10: 3 residues within 4Å: Chain G: V.16 Ligands: F09.8, F09.12 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.16 F09.12: 4 residues within 4Å: Chain G: F.5, A.12 Ligands: F09.10, F09.14 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:A.12 F09.14: 3 residues within 4Å: Chain H: A.13 Ligands: F09.12, F09.16 No protein-ligand interaction detected (PLIP) F09.16: 3 residues within 4Å: Chain J: V.16 Ligands: F09.14, F09.18 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.16 F09.18: 4 residues within 4Å: Chain J: F.5, V.9, A.13 Ligands: F09.16 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.9 F09.20: 2 residues within 4Å: Chain K: F.5, A.13 No protein-ligand interaction detected (PLIP) F09.22: 2 residues within 4Å: Chain A: F.5 Ligands: F09.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meier, T. et al., Complete Ion-Coordination Structure in the Rotor Ring of Na(+)-Dependent F-ATP Synthases. J.Mol.Biol. (2009)

Release Date

2009-06-09

Peptides

ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC: 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, SODIUM ION SPECIFIC

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