SMTL ID : 7o0d.1

monomeric acetyl-CoA synthase in open conformation with methanethiol moiety of CoA bound to nickel proximal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: C.511, L.513, C.514, H.521, C.523, V.525, G.531, L.532, C.533, I.536, C.600, C.602 Ligands: NI.2, MEE.4 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.511, A:C.514, A:C.523, A:C.533

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

NI.2: 9 residues within 4Å: Chain A: C.514, F.517, L.532, C.533, C.600, C.602 Ligands: SF4.1, NI.3, MEE.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.514, A:C.600, A:C.602 NI.3: 7 residues within 4Å: Chain A: F.517, L.532, C.600, G.601, C.602, F.603 Ligands: NI.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.600, A:C.602

1 x MEE: METHANETHIOL(Non-covalent)

MEE.4: 7 residues within 4Å: Chain A: L.513, C.514, F.517, C.533, C.602 Ligands: SF4.1, NI.2 No protein-ligand interaction detected (PLIP)

4 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.5: 7 residues within 4Å: Chain A: E.42, I.43, L.45, S.46, I.49, E.50, V.85 No protein-ligand interaction detected (PLIP) PG6.9: 14 residues within 4Å: Chain A: E.119, R.122, Y.123, I.132, V.133, V.134, W.137, G.139, F.140, L.214, G.215, N.216, Q.219, H.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.122 Water bridges: A:Q.219, A:Q.219 PG6.19: 6 residues within 4Å: Chain A: I.562, D.563, Q.568, R.586, E.594, Y.595 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.568, A:R.586, A:R.586 PG6.23: 8 residues within 4Å: Chain A: S.74, E.76, K.82, D.83, P.86, R.90, G.240 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.90, A:R.90

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 8 residues within 4Å: Chain A: I.151, M.233, F.234, F.517, G.601, C.602, R.621 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.233, A:R.621 PG4.10: 6 residues within 4Å: Chain A: E.503, P.564, V.565, Y.590, K.661, K.664 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.664 Water bridges: A:K.661

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

PEG.7: 5 residues within 4Å: Chain A: A.238, P.239, G.240, L.241 Ligands: PG6.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.240 PEG.8: 7 residues within 4Å: Chain A: I.629, M.631, L.636, M.639, V.640, T.646, F.649 No protein-ligand interaction detected (PLIP) PEG.20: 4 residues within 4Å: Chain A: E.731, P.732, L.733, L.734 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.732 PEG.22: 5 residues within 4Å: Chain A: I.12, R.250, V.313, R.314, G.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.250, A:R.250

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

SO4.11: 2 residues within 4Å: Chain A: K.51, K.125 7 PLIP interactions: 7 interactions with chain A Water bridges: A:Y.52, A:K.125, A:K.125, A:K.125, A:K.125 Salt bridges: A:K.51, A:K.125 SO4.12: 3 residues within 4Å: Chain A: K.96, S.97, E.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.97, A:S.97 Water bridges: A:Y.31, A:I.95 SO4.13: 3 residues within 4Å: Chain A: R.621, F.633 Ligands: PG4.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.621 SO4.14: 5 residues within 4Å: Chain A: R.167, D.170, S.171, Q.197, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.171, A:Q.197 Salt bridges: A:R.167 SO4.15: 6 residues within 4Å: Chain A: R.410, V.530, G.534, A.535, S.537, D.540 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.534, A:S.537, A:S.537 Water bridges: A:S.655 Salt bridges: A:R.410 SO4.16: 5 residues within 4Å: Chain A: V.505, D.506, T.507, W.538, K.542 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.506, A:D.506, A:T.507 Salt bridges: A:K.542

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.17: 11 residues within 4Å: Chain A: H.56, P.57, V.58, G.59, Y.60, P.61, Y.123, L.124, H.126, T.127, P.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.123 Water bridges: A:G.59, A:D.62, A:H.126 MES.18: 6 residues within 4Å: Chain A: A.670, E.694, G.695, L.696, P.726, M.730 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.694 Water bridges: A:P.726 MES.21: 3 residues within 4Å: Chain A: R.671, M.730, E.731 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.671, A:E.731

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
A

CO-methylating acetyl-CoA synthase

Related Entries With Identical Sequence