SMTL ID : 4cbj.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 2.80 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, E.30 Chain M: V.15 Ligands: DPV.3, DPV.17 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain M, 2 interactions with chain A Salt bridges: B:K.26, B:E.30, A:K.26, A:E.30 Hydrophobic interactions: M:V.15 DPV.3: 8 residues within 4Å: Chain A: L.12, V.15, I.23 Chain B: K.26 Chain C: K.26 Ligands: DPV.1, DPV.4, DPV.5 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:L.12, A:I.23 Salt bridges: B:K.26, C:K.26 DPV.4: 8 residues within 4Å: Chain B: I.23 Chain C: I.23, K.26, E.30 Chain D: K.26, E.30 Ligands: DPV.3, DPV.5 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 3 interactions with chain C Salt bridges: D:K.26, D:E.30, C:K.26, C:E.30 Hydrophobic interactions: B:I.23, C:I.23 DPV.5: 4 residues within 4Å: Chain C: I.23 Ligands: DPV.3, DPV.4, DPV.7 No protein-ligand interaction detected (PLIP) DPV.7: 7 residues within 4Å: Chain D: I.23 Chain E: V.15, I.19, K.26 Chain F: K.26 Ligands: DPV.5, DPV.8 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: E:V.15, E:I.19, D:I.23 Salt bridges: E:K.26, F:K.26 DPV.8: 8 residues within 4Å: Chain E: V.15 Chain F: I.19, I.23, K.26, E.30 Chain G: K.26 Ligands: DPV.7, DPV.9 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: F:I.19, E:V.15 Salt bridges: F:K.26, F:E.30, G:K.26 DPV.9: 9 residues within 4Å: Chain F: V.15, I.23 Chain G: I.23, K.26, E.30 Chain H: K.26, E.30 Ligands: DPV.8, DPV.10 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F, 1 interactions with chain H Salt bridges: G:E.30, H:K.26 Hydrophobic interactions: F:V.15 DPV.10: 6 residues within 4Å: Chain G: V.15 Chain H: I.23, K.26 Chain I: K.26 Ligands: DPV.9, DPV.11 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H Salt bridges: I:K.26, H:K.26 DPV.11: 6 residues within 4Å: Chain H: V.15 Chain I: I.23, K.26 Chain J: K.26 Ligands: DPV.10, DPV.12 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J, 1 interactions with chain H Salt bridges: I:K.26, I:E.30, J:K.26 Hydrophobic interactions: H:V.15 DPV.12: 8 residues within 4Å: Chain I: V.15, I.23 Chain J: I.23, K.26 Chain K: K.26, E.30 Ligands: DPV.11, DPV.14 6 PLIP interactions: 2 interactions with chain J, 2 interactions with chain K, 2 interactions with chain I Salt bridges: J:K.26, J:E.30, K:K.26, K:E.30 Hydrophobic interactions: I:V.15, I:I.23 DPV.14: 9 residues within 4Å: Chain J: V.15, I.23 Chain K: V.15, I.19, I.23, K.26 Chain L: K.26 Ligands: DPV.12, DPV.16 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 2 interactions with chain J Salt bridges: L:K.26 Hydrophobic interactions: K:V.15, K:I.19, J:V.15, J:I.23 DPV.16: 8 residues within 4Å: Chain K: V.15, I.23 Chain L: V.15, I.23, K.26 Chain M: K.26 Ligands: DPV.14, DPV.17 4 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 1 interactions with chain M Hydrogen bonds: L:I.23 Hydrophobic interactions: K:V.15, K:I.23 Salt bridges: M:K.26 DPV.17: 7 residues within 4Å: Chain A: K.26 Chain L: V.15, I.23 Chain M: I.23, K.26 Ligands: DPV.1, DPV.16 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain A, 1 interactions with chain M Hydrophobic interactions: L:V.15, L:I.23 Salt bridges: A:K.26, M:K.26

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

TAM.2: 6 residues within 4Å: Chain A: T.33, R.34, Q.35, P.36 Chain M: R.34, Q.35 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain M Hydrophobic interactions: A:P.36 Hydrogen bonds: A:Q.35, M:R.34, M:Q.35, M:Q.35 TAM.6: 3 residues within 4Å: Chain C: Q.35 Chain D: R.34, Q.35 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.35, D:R.34, D:Q.35 TAM.15: 4 residues within 4Å: Chain K: R.34, Q.35, P.36, E.37 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.34, K:E.37

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

LMT.13: 3 residues within 4Å: Chain J: F.3, L.68, F.69 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:F.69, J:F.69, J:F.69

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

2014-05-28

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