SMTL ID : 3day.1

Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP-CPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: M.476, H.478, P.479, V.481 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:M.476, A:H.478, H2O.9, H2O.10, H2O.10 MG.2: 2 residues within 4Å: Chain A: K.222 Ligands: APC.6 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: P.305, R.309, S.333, L.335, T.338 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: L.281, P.282, K.283, F.284, D.285, V.288 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: S.41, D.42, H.46 Ligand excluded by PLIP

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.6: 23 residues within 4Å: Chain A: T.214, S.215, G.216, T.217, S.218, K.222, G.331, E.332, S.333, E.352, S.353, Y.354, G.355, Q.356, T.357, M.376, D.439, F.451, R.454, K.550 Ligands: MG.2, UNX.11, UNX.15 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:T.214, A:S.215, A:G.216, A:T.217, A:T.217, A:S.218, A:S.218, A:G.331, A:E.352, A:E.352, A:G.355, A:Q.356, A:T.357, A:T.357, A:T.357, A:D.439, A:R.454, A:R.454, A:K.550 Water bridges: A:S.215, A:S.218, A:K.222, A:K.222, A:K.222, A:K.222, A:E.332, A:S.333, A:L.437 Salt bridges: A:K.222 pi-Stacking: A:Y.354

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 3 residues within 4Å: Chain A: M.73, W.74, E.78 5 PLIP interactions: 5 interactions with chain A Water bridges: A:M.73, A:M.73, A:M.73, A:N.75, A:E.78

11 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 8 residues within 4Å: Chain A: I.259, G.355, Q.356, T.357 Ligands: UNX.9, UNX.10, UNX.11, UNX.15 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: L.263 Ligands: UNX.8, UNX.10 No protein-ligand interaction detected (PLIP) UNX.10: 7 residues within 4Å: Chain A: I.259, Q.356, G.360 Ligands: UNX.8, UNX.9, UNX.11, UNX.15 No protein-ligand interaction detected (PLIP) UNX.11: 7 residues within 4Å: Chain A: G.331, G.355 Ligands: APC.6, UNX.8, UNX.10, UNX.12, UNX.15 No protein-ligand interaction detected (PLIP) UNX.12: 5 residues within 4Å: Chain A: V.330, G.331 Ligands: UNX.11, UNX.13, UNX.14 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain A: W.258 Ligands: UNX.12, UNX.14, UNX.18 No protein-ligand interaction detected (PLIP) UNX.14: 6 residues within 4Å: Chain A: W.258, I.259, L.260 Ligands: UNX.12, UNX.13, UNX.15 No protein-ligand interaction detected (PLIP) UNX.15: 7 residues within 4Å: Chain A: I.259, T.357 Ligands: APC.6, UNX.8, UNX.10, UNX.11, UNX.14 No protein-ligand interaction detected (PLIP) UNX.16: 3 residues within 4Å: Chain A: D.255, W.258 Ligands: UNX.17 No protein-ligand interaction detected (PLIP) UNX.17: 5 residues within 4Å: Chain A: S.254, D.255, W.258 Ligands: UNX.16, UNX.18 No protein-ligand interaction detected (PLIP) UNX.18: 6 residues within 4Å: Chain A: S.254, D.255, W.258, L.260 Ligands: UNX.13, UNX.17 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 7 residues within 4Å: Chain A: W.64, K.70, L.72, V.109, P.110, E.111, K.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kochan, G. et al., Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A. J.Mol.Biol. (2009)

Release Date

2008-07-15

Peptides

Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor

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