SMTL ID : 4cbk.1

The c-ring ion binding site of the ATP synthase from Bacillus pseudofirmus OF4 is adapted to alkaliphilic cell physiology

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-13-mer

Ligands

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

DPV.1: 7 residues within 4Å: Chain A: K.26, E.30 Chain B: K.26 Chain M: L.12, V.15 Ligands: DPV.3, DPV.24 7 PLIP interactions: 2 interactions with chain A, 2 interactions with chain M, 3 interactions with chain B Salt bridges: A:K.26, A:E.30, B:K.26 Hydrophobic interactions: M:L.12, M:V.15 Water bridges: B:K.26, B:K.26 DPV.3: 7 residues within 4Å: Chain A: I.23 Chain B: I.19, I.23, K.26 Chain C: K.26 Ligands: DPV.1, DPV.6 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:I.23, B:I.19 Salt bridges: C:K.26, B:K.26, B:E.30 DPV.6: 7 residues within 4Å: Chain C: I.23, K.26, E.30 Chain D: K.26, E.30 Ligands: DPV.3, DPV.8 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:K.26, D:E.30, C:K.26, C:E.30 DPV.8: 7 residues within 4Å: Chain D: K.26, E.30 Chain E: K.26, E.30 Ligands: DPV.6, NA.7, DPV.10 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Salt bridges: D:K.26, D:E.30, E:K.26, E:E.30 DPV.10: 7 residues within 4Å: Chain D: V.15, I.23 Chain E: I.19, K.26 Chain F: K.26 Ligands: DPV.8, DPV.12 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: D:V.15, D:I.23, E:I.19 Salt bridges: E:K.26, F:K.26 DPV.12: 10 residues within 4Å: Chain E: I.23 Chain F: I.19, I.23, K.26, E.30 Chain G: K.26, E.30 Ligands: DPV.10, NA.11, DPV.14 7 PLIP interactions: 4 interactions with chain F, 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: F:I.19, F:I.19, E:I.23 Salt bridges: F:K.26, F:E.30, G:K.26, G:E.30 DPV.14: 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.12, DPV.16 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G, 2 interactions with chain F Salt bridges: H:K.26, H:E.30, G:E.30 Hydrophobic interactions: F:V.15, F:I.23 DPV.16: 8 residues within 4Å: Chain G: V.15 Chain H: I.23, K.26, E.30 Chain I: K.26, E.30 Ligands: DPV.14, DPV.18 7 PLIP interactions: 2 interactions with chain H, 4 interactions with chain I, 1 interactions with chain G Salt bridges: H:K.26, H:E.30, I:K.26, I:E.30 Water bridges: I:K.26, I:K.26 Hydrophobic interactions: G:V.15 DPV.18: 6 residues within 4Å: Chain H: I.23 Chain I: I.19, K.26 Chain J: K.26 Ligands: DPV.16, DPV.19 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain H, 2 interactions with chain I Salt bridges: J:K.26, I:K.26 Hydrophobic interactions: H:I.23, I:I.19 DPV.19: 7 residues within 4Å: Chain I: I.23 Chain J: K.26, E.30 Chain K: K.26, E.30 Ligands: DPV.18, DPV.21 5 PLIP interactions: 2 interactions with chain J, 2 interactions with chain K, 1 interactions with chain I Salt bridges: J:K.26, J:E.30, K:K.26, K:E.30 Hydrophobic interactions: I:I.23 DPV.21: 5 residues within 4Å: Chain K: I.23, K.26 Chain L: K.26 Ligands: DPV.19, DPV.23 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:I.23 Salt bridges: K:K.26, L:K.26 Water bridges: L:K.26 DPV.23: 8 residues within 4Å: Chain K: V.15, I.23 Chain L: V.15, I.23, K.26 Chain M: K.26 Ligands: DPV.21, DPV.24 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K, 1 interactions with chain M Hydrophobic interactions: L:V.15, K:I.23 Salt bridges: L:K.26, M:K.26 DPV.24: 6 residues within 4Å: Chain A: K.26 Chain M: I.23, K.26, E.30 Ligands: DPV.1, DPV.23 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain A Salt bridges: M:K.26, M:E.30, A:K.26

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

NA.2: 3 residues within 4Å: Chain B: A.27, E.30 Chain C: E.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.30 NA.5: 4 residues within 4Å: Chain C: A.27, E.30 Chain D: K.26, E.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.30, C:E.30 NA.7: 4 residues within 4Å: Chain D: A.27, E.30 Chain E: E.30 Ligands: DPV.8 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.30, D:E.30 NA.9: 3 residues within 4Å: Chain E: A.27, E.30 Chain F: E.30 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.30, E:E.30 NA.11: 5 residues within 4Å: Chain F: A.27, E.30 Chain G: K.26, E.30 Ligands: DPV.12 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:K.26, F:E.30 NA.13: 3 residues within 4Å: Chain G: A.27, E.30 Chain H: E.30 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.30, G:E.30 NA.15: 4 residues within 4Å: Chain H: A.27, E.30 Chain I: K.26, E.30 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.30 NA.17: 3 residues within 4Å: Chain I: A.27, E.30 Chain J: E.30 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:E.30, J:E.30 NA.20: 3 residues within 4Å: Chain K: E.30 Chain L: K.26, E.30 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.30, L:E.30 NA.22: 3 residues within 4Å: Chain L: A.27, E.30 Chain M: E.30 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:E.30, M:E.30

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.4: 5 residues within 4Å: Chain B: E.37, L.38, T.41 Chain C: P.36, R.39 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:P.36, C:R.39 Hydrophobic interactions: B:E.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Preiss, L. et al., The C-Ring Ion-Binding Site of the ATP Synthase from Bacillus Pseudofirmus of4 is Adapted to Alkaliphilic Lifestyle. Mol.Microbiol. (2014)

Release Date

2014-04-23

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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