SMTL ID : 1yce.4 (3 other biounits)

Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-11-mer

Ligands

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

NA.1: 8 residues within 4Å: Chain A: P.28, G.29, Q.32, E.65 Chain K: V.63, A.64, S.66, T.67 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:T.67, K:T.67 NA.3: 4 residues within 4Å: Chain A: V.63, S.66 Chain B: Q.32, E.65 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.32, B:E.65, A:S.66, A:T.67 NA.5: 6 residues within 4Å: Chain B: V.63, A.64, S.66, T.67 Chain C: Q.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:Q.32 NA.7: 6 residues within 4Å: Chain C: V.63, A.64, S.66, T.67 Chain D: Q.32, E.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.63, C:T.67 NA.9: 7 residues within 4Å: Chain D: V.63, A.64, S.66, T.67 Chain E: P.28, Q.32, E.65 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:A.64, D:S.66, D:T.67, E:Q.32 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: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:Q.32, E:A.64, E:S.66, E:T.67 NA.13: 5 residues within 4Å: Chain F: V.63, A.64, S.66 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: 2 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:Q.32, H:E.65, G:S.66, G:T.67 NA.17: 5 residues within 4Å: Chain H: V.63, S.66, T.67 Chain I: Q.32, E.65 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:Q.32, H:A.64, H:S.66, H:T.67 NA.19: 5 residues within 4Å: Chain I: V.63, S.66, T.67 Chain J: Q.32, E.65 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:Q.32, I:V.63, I:S.66, I:T.67 NA.21: 5 residues within 4Å: Chain J: V.63, S.66, T.67 Chain K: Q.32, E.65 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:V.63, J:S.66, J:T.67, K:Q.32

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meier, T. et al., Structure of the rotor ring of F-Type Na+-ATPase from Ilyobacter tartaricus. Science (2005)

Release Date

2005-04-12

Peptides

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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subunit c

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