SMTL ID : 3nd8.1

Structural characterization for the nucleotide binding ability of subunit A of the A1AO ATP synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 5 residues within 4Å: Chain A: V.242, Q.246, K.249, L.278, A.507 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.242, A:L.278 Hydrogen bonds: A:Q.246, A:K.249, A:K.249 MRD.2: 6 residues within 4Å: Chain A: D.420, L.421, R.424, N.431, W.432, L.433 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.421, A:W.432 Hydrogen bonds: A:D.420 Water bridges: A:N.431, A:Q.473 MRD.3: 4 residues within 4Å: Chain A: K.198, P.200, Y.201, K.202 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.198, A:Y.201 Water bridges: A:K.198 MRD.7: 5 residues within 4Å: Chain A: E.555, R.558, E.562, K.567, L.571 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.562, A:L.571

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 4 residues within 4Å: Chain A: M.458, K.461, L.528, D.532 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.461 Hydrogen bonds: A:K.461, A:K.461 Water bridges: A:R.525 MPD.8: 3 residues within 4Å: Chain A: D.252, Y.514, P.517 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.252 Water bridges: A:D.252

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 4 residues within 4Å: Chain A: R.424, R.499, E.500, Q.504 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.500 Hydrogen bonds: A:R.499, A:E.500, A:Q.504

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: A.240, T.241, D.418, A.419, A.422 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manimekalai, M.S. et al., The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase. J.Mol.Biol. (2011)

Release Date

2011-03-30

Peptides

V-type ATP synthase alpha chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

V-type ATP synthase alpha chain