SMTL ID : 7nys.2 (1 other biounit)

monomeric acetyl-CoA synthase in closed conformation with carbon monoxide bound to the Ni proximal of cluster A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: I.150, C.510, L.512, C.513, H.520, C.522, G.530, L.531, C.532, I.535, C.601 Ligands: UWE.2 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.510, A:C.513, A:C.522, A:C.532

1 x UWE: $l^{3}-oxidanylidynemethylnickel(Non-covalent)

UWE.2: 9 residues within 4Å: Chain A: G.149, I.150, V.153, F.233, C.513, C.599, C.601 Ligands: SF4.1, NI.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.513, A:C.599, A:C.601, UWE.2

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 7 residues within 4Å: Chain A: F.233, L.531, C.599, G.600, C.601, F.602 Ligands: UWE.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.599, A:C.601

1 x UW8: 2-[3,8,8,12,12-pentakis(2-hydroxy-2-oxoethyl)-2,7,11-tris(oxidanylidene)-1,4,6,9,10,13-hexaoxa-5$l^{6}-titanaspiro[4.4^{5}.4^{5}]tridecan-3-yl]ethanoic acid(Non-covalent)

UW8.4: 3 residues within 4Å: Chain A: K.50, Y.51, K.124 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.50, A:K.124 Hydrogen bonds: A:K.50, A:Y.51, A:K.124 Salt bridges: A:K.50, A:K.50, A:K.50, A:K.50, A:K.50, A:K.124, A:K.124, A:K.124, A:K.124, A:K.124

5 x MLI: MALONATE ION(Non-functional Binders)

MLI.5: 2 residues within 4Å: Chain A: K.339, K.350 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.350 Salt bridges: A:K.339, A:K.339, A:K.350 MLI.6: 7 residues within 4Å: Chain A: G.58, Y.59, P.60, Y.122, H.125, T.126, P.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.59 Water bridges: A:H.125 Salt bridges: A:H.125 MLI.9: 5 residues within 4Å: Chain A: R.497, L.499, S.500, E.527, R.659 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.660 Salt bridges: A:R.659, A:R.659 MLI.10: 4 residues within 4Å: Chain A: K.203, D.341, S.435, E.437 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.341, A:D.341, A:S.435, A:E.437 Water bridges: A:K.203, A:K.203, A:E.437 Salt bridges: A:K.203, A:K.203 MLI.11: 6 residues within 4Å: Chain A: Y.608, P.610, N.613, P.731, L.732, L.733 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.610, A:P.731 Hydrogen bonds: A:Y.608, A:L.732, A:L.732, A:L.732

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 1 residues within 4Å: Chain A: E.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.381 PEG.8: 4 residues within 4Å: Chain A: R.486, K.487, A.490, E.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.491 PEG.12: 5 residues within 4Å: Chain A: I.6, L.240, R.241, D.242, A.243 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.241, A:R.241, A:D.242, A:A.243 Water bridges: A:D.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kreibich, J. et al., Ligand binding at the Ni,Ni-[4Fe-4S] cluster of acetyl-CoA synthase. To Be Published

Release Date

2022-04-13

Peptides

CO-methylating acetyl-CoA synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

CO-methylating acetyl-CoA synthase

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