SMTL ID : 2x2v.1

Structural basis of a novel proton-coordination type in an F1Fo-ATP synthase rotor ring

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-13-mer

Ligands

13 x DPV: dodecyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

DPV.1: 5 residues within 4Å: Chain A: I.23, K.26 Chain B: K.26 Ligands: DPV.3, DPV.23 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.26, B:K.26 Water bridges: B:K.26 DPV.3: 8 residues within 4Å: Chain B: I.19, I.23, K.26, E.30 Chain C: K.26, E.30 Ligands: DPV.1, DPV.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.19 Salt bridges: B:K.26, B:E.30, C:K.26 Water bridges: C:K.26 DPV.5: 6 residues within 4Å: Chain C: I.23, K.26 Chain D: K.26, E.30 Ligands: DPV.3, DPV.7 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:K.26, D:K.26 DPV.7: 10 residues within 4Å: Chain C: I.19, I.23 Chain D: I.19, K.26, E.30 Chain E: K.26, E.30 Ligands: DPV.5, NA.6, DPV.9 7 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D, 2 interactions with chain C Salt bridges: E:K.26, E:E.30, D:K.26, D:E.30 Hydrophobic interactions: D:I.19, C:I.19, C:I.23 DPV.9: 6 residues within 4Å: Chain D: I.23 Chain E: I.23, K.26 Chain F: K.26 Ligands: DPV.7, DPV.11 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Water bridges: E:K.26 Salt bridges: E:K.26, F:K.26 Hydrophobic interactions: D:I.23 DPV.11: 9 residues within 4Å: Chain E: V.15, I.23 Chain F: I.23, K.26, E.30 Chain G: K.26, E.30 Ligands: DPV.9, DPV.12 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G, 1 interactions with chain E Water bridges: F:I.23 Salt bridges: F:K.26, F:E.30, G:K.26 Hydrophobic interactions: E:V.15 DPV.12: 9 residues within 4Å: Chain F: V.15, I.23 Chain G: I.19, K.26, E.30 Chain H: K.26, E.30 Ligands: DPV.11, DPV.14 7 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F, 2 interactions with chain H Hydrophobic interactions: G:I.19, F:V.15, F:I.23 Salt bridges: G:K.26, G:E.30, H:K.26, H:E.30 DPV.14: 7 residues within 4Å: Chain G: V.15 Chain H: I.23, K.26, E.30 Chain I: K.26 Ligands: DPV.12, DPV.16 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain I, 1 interactions with chain G Salt bridges: H:K.26, H:E.30, I:K.26, I:E.30 Hydrophobic interactions: G:V.15 DPV.16: 6 residues within 4Å: Chain H: V.15, I.23 Chain I: K.26 Chain J: K.26 Ligands: DPV.14, DPV.18 7 PLIP interactions: 2 interactions with chain H, 3 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: H:V.15, H:I.23 Water bridges: J:K.26, J:K.26, I:K.26 Salt bridges: J:K.26, I:K.26 DPV.18: 10 residues within 4Å: Chain I: V.15, I.23 Chain J: V.15, I.23, K.26, E.30 Chain K: K.26, E.30 Ligands: DPV.16, DPV.20 7 PLIP interactions: 2 interactions with chain K, 3 interactions with chain J, 2 interactions with chain I Salt bridges: K:K.26, K:E.30, J:K.26, J:E.30 Hydrophobic interactions: J:V.15, I:V.15, I:I.23 DPV.20: 9 residues within 4Å: Chain J: V.15, I.23 Chain K: I.23, K.26, E.30 Chain L: K.26, E.30 Ligands: DPV.18, DPV.22 6 PLIP interactions: 2 interactions with chain K, 2 interactions with chain L, 2 interactions with chain J Salt bridges: K:K.26, K:E.30, L:K.26 Water bridges: L:K.26 Hydrophobic interactions: J:V.15, J:I.23 DPV.22: 5 residues within 4Å: Chain K: V.15 Chain L: I.23, K.26 Ligands: DPV.20, DPV.23 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain L Water bridges: M:K.26 Salt bridges: M:K.26, L:K.26 DPV.23: 9 residues within 4Å: Chain A: K.26, E.30 Chain L: L.12 Chain M: I.19, I.23, K.26, E.30 Ligands: DPV.1, DPV.22 7 PLIP interactions: 4 interactions with chain M, 1 interactions with chain L, 2 interactions with chain A Hydrophobic interactions: M:I.19, M:I.19, L:L.12 Salt bridges: M:K.26, M:E.30, A:K.26, A:E.30

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

NA.2: 3 residues within 4Å: Chain B: A.27, E.30 Chain C: E.30 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.30, C:E.30 Water bridges: C:K.26 NA.4: 4 residues within 4Å: Chain C: A.27, E.30 Chain D: K.26, E.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.30 NA.6: 5 residues within 4Å: Chain D: A.27, E.30 Chain E: K.26, E.30 Ligands: DPV.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.30 NA.8: 4 residues within 4Å: Chain E: A.27, E.30 Chain F: K.26, E.30 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.30 NA.10: 4 residues within 4Å: Chain F: A.27, E.30 Chain G: K.26, E.30 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.30 NA.13: 3 residues within 4Å: Chain H: A.27, E.30 Chain I: E.30 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.30, H:E.30 NA.15: 4 residues within 4Å: Chain I: A.27, E.30 Chain J: K.26, E.30 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.30 Water bridges: J:K.26 NA.17: 3 residues within 4Å: Chain J: A.27, E.30 Chain K: E.30 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:E.30, J:E.30 Water bridges: J:E.30 NA.19: 4 residues within 4Å: Chain K: A.27, E.30 Chain L: K.26, E.30 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:K.26, L:E.30 NA.21: 4 residues within 4Å: Chain L: A.27, E.30 Chain M: K.26, E.30 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:E.30, M:E.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Preiss, L. et al., A New Type of Proton Coordination in an F(1)F(O)- ATP Synthase Rotor Ring. Plos Biol. (2010)

Release Date

2010-08-18

Peptides

ATP SYNTHASE SUBUNIT C: ABCDEFGHIJKLM

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

L
L

M
M

Membrane

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

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