SMTL ID : 4bem.1

Crystal structure of the F-type ATP synthase c-ring from Acetobacterium woodii.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-9-1-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: Q.29, E.62 Chain J: V.160, T.163, T.164 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrogen bonds: J:V.160, J:T.163, J:T.164, A:Q.29 NA.2: 6 residues within 4Å: Chain A: V.60, A.61, T.63, T.64 Chain B: Q.29, E.62 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.63, A:T.64, B:Q.29, B:E.62 NA.4: 4 residues within 4Å: Chain B: V.60, T.63 Chain C: Q.29, E.62 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.63, B:T.64, C:Q.29, C:Q.29 NA.7: 6 residues within 4Å: Chain C: V.60, A.61, T.63, T.64 Chain D: Q.29, E.62 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.63, C:T.64, D:Q.29, D:Q.29 NA.8: 5 residues within 4Å: Chain D: V.60, A.61, T.63 Chain E: Q.29, E.62 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:T.63, D:T.64, E:Q.29, E:E.62 NA.12: 5 residues within 4Å: Chain E: V.60, A.61, T.63 Chain F: Q.29, E.62 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:Q.29, F:E.62, E:T.63, E:T.64 NA.15: 5 residues within 4Å: Chain F: V.60, A.61, T.63 Chain G: Q.29, E.62 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:T.63, F:T.63, F:T.64, G:Q.29 NA.20: 5 residues within 4Å: Chain G: V.60, A.61, T.63 Chain H: Q.29, E.62 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:T.63, G:T.63, G:T.64, H:Q.29 NA.23: 5 residues within 4Å: Chain H: V.60, A.61, T.63 Chain I: Q.29, E.62 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:T.63, H:T.64, I:Q.29, I:E.62 NA.30: 6 residues within 4Å: Chain I: V.60, A.61, T.63, T.64 Chain J: Q.46, E.79 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:T.63, I:T.64, J:Q.46, J:E.79

19 x HTG: heptyl 1-thio-beta-D-glucopyranoside(Non-functional Binders)(Non-covalent)

HTG.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HTG.10: 3 residues within 4Å: Chain D: P.80 Chain E: L.73, F.77 Ligand excluded by PLIP HTG.11: 3 residues within 4Å: Chain E: L.56, V.60 Chain F: I.51 Ligand excluded by PLIP HTG.13: 5 residues within 4Å: Chain E: V.60 Chain F: R.52, L.56, A.59, E.62 Ligand excluded by PLIP HTG.17: 5 residues within 4Å: Chain G: I.74, A.78 Chain H: F.77 Ligands: ACT.16, HTG.21 Ligand excluded by PLIP HTG.18: 2 residues within 4Å: Chain G: R.52 Ligands: HTG.19 Ligand excluded by PLIP HTG.19: 6 residues within 4Å: Chain F: V.60, Y.67 Chain G: L.55, A.59, E.62 Ligands: HTG.18 Ligand excluded by PLIP HTG.21: 5 residues within 4Å: Chain H: L.73, F.77, A.78 Ligands: HTG.17, HTG.22 Ligand excluded by PLIP HTG.22: 6 residues within 4Å: Chain H: I.74, F.77, A.78 Chain I: F.77 Ligands: HTG.21, HTG.26 Ligand excluded by PLIP HTG.26: 4 residues within 4Å: Chain I: L.73, F.77 Ligands: HTG.22, HTG.27 Ligand excluded by PLIP HTG.27: 6 residues within 4Å: Chain I: I.70, L.73, I.74, F.77, A.78 Ligands: HTG.26 Ligand excluded by PLIP HTG.28: 4 residues within 4Å: Chain I: R.52, L.55, L.56, A.59 Ligand excluded by PLIP HTG.29: 5 residues within 4Å: Chain I: R.52, L.56 Chain J: N.65, V.68, L.72 Ligand excluded by PLIP HTG.31: 4 residues within 4Å: Chain J: M.69, L.73, V.77 Ligands: HTG.34 Ligand excluded by PLIP HTG.32: 6 residues within 4Å: Chain A: I.51 Chain J: R.152, L.155, L.156 Ligands: HTG.33, HTG.34 Ligand excluded by PLIP HTG.33: 6 residues within 4Å: Chain A: I.51, L.55, A.59 Chain J: L.156, V.160 Ligands: HTG.32 Ligand excluded by PLIP HTG.34: 6 residues within 4Å: Chain J: V.77, Q.158, A.159, Q.162 Ligands: HTG.31, HTG.32 Ligand excluded by PLIP HTG.35: 4 residues within 4Å: Chain J: F.84, V.87, I.91, Y.177 Ligand excluded by PLIP HTG.36: 10 residues within 4Å: Chain G: M.1, G.3, F.6 Chain H: E.2, F.6 Chain I: M.1 Chain J: F.10, V.11, F.14 Ligands: ACT.14 Ligand excluded by PLIP

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 2 residues within 4Å: Chain C: E.2 Chain D: M.1 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.2, H2O.2

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

TAM.6: 3 residues within 4Å: Chain C: D.49 Chain D: P.44, Q.47 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.44, D:Q.47

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.9: 6 residues within 4Å: Chain D: R.42, Q.43, E.45 Chain E: R.42, Q.43, E.45 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:E.45, E:E.45 Water bridges: E:R.42

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 3 residues within 4Å: Chain F: M.1 Chain G: M.1 Ligands: HTG.36 No protein-ligand interaction detected (PLIP) ACT.16: 4 residues within 4Å: Chain G: A.78, N.79, F.82 Ligands: HTG.17 1 PLIP interactions: 1 interactions with chain G Water bridges: G:N.79 ACT.24: 3 residues within 4Å: Chain I: E.2, G.3, L.4 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:D.22, I:G.3, I:L.4 ACT.25: 4 residues within 4Å: Chain I: F.77, A.78, N.79, F.82 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.79, I:F.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matthies, D. et al., High-Resolution Structure and Mechanism of an F/V-Hybrid Rotor Ring in a Na+-Coupled ATP Synthase. Nat.Commun. (2014)

Release Date

2014-03-26

Peptides

F1FO ATPASE C2 SUBUNIT: ABCDEFGHI
F1FO ATPASE C1 SUBUNIT: J

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

Membrane

We predict this structure to be a membrane protein.
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F1FO ATPASE C2 SUBUNIT

F1FO ATPASE C1 SUBUNIT