SMTL ID : 5txr.1

Structure of ALAS from S. cerevisiae non-covalently bound to PLP cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 5 residues within 4Å: Chain A: L.150, M.200, A.201, R.402, L.445 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.402, A:R.402 Water bridges: A:A.201 FMT.2: 7 residues within 4Å: Chain A: R.34, T.395 Chain B: T.93, N.95, I.96, I.307, F.308 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.93, A:R.34, A:R.34, A:T.395, A:T.395 Water bridges: B:N.95, B:N.95 FMT.3: 5 residues within 4Å: Chain A: F.46, A.68, K.71, P.409, G.410 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.71 Water bridges: A:F.46 FMT.4: 5 residues within 4Å: Chain A: E.74, R.325, Y.326, C.329, H.330 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.74, A:E.74, A:Y.326 FMT.8: 7 residues within 4Å: Chain B: L.150, H.171, Y.198, M.200, A.201, G.202, S.203 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:M.200, B:A.201, B:G.202, B:S.203, B:S.203 Water bridges: B:S.199 FMT.9: 5 residues within 4Å: Chain B: R.249, A.250, D.470, N.472, P.473 No protein-ligand interaction detected (PLIP) FMT.10: 5 residues within 4Å: Chain A: K.160, H.161 Chain B: K.160, H.161, N.163 No protein-ligand interaction detected (PLIP) FMT.11: 6 residues within 4Å: Chain B: E.208, C.243, D.244, N.259, D.260, K.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.259, B:D.260, B:K.261 FMT.12: 6 residues within 4Å: Chain B: S.147, D.148, E.149, N.151, I.156, I.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.147, B:S.147 Water bridges: B:K.166 FMT.13: 8 residues within 4Å: Chain B: H.152, E.195, V.197, Y.198, S.199, M.200, H.227 Ligands: PLP.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.195, B:S.199, B:S.199, B:H.227 Water bridges: B:M.200, B:M.200

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.5: 16 residues within 4Å: Chain A: S.124, C.125, Y.126, N.129, H.152, S.154, E.195, D.224, V.226, H.227, T.277, K.280, G.286 Chain B: F.308, T.309, T.310 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.152, A:V.226 Hydrogen bonds: A:S.124, A:C.125, A:Y.126, A:N.129, A:H.152, A:S.154, A:H.227, A:T.277, A:T.277, A:K.280, B:T.309, B:T.310, B:T.310 Water bridges: A:S.199, B:S.123 Salt bridges: A:K.280 pi-Stacking: A:H.152 PLP.14: 17 residues within 4Å: Chain A: F.308, T.309, T.310 Chain B: S.124, C.125, Y.126, N.129, H.152, S.154, E.195, D.224, V.226, H.227, T.277, K.280, G.286 Ligands: FMT.13 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:H.152, B:V.226 Hydrogen bonds: B:C.125, B:Y.126, B:N.129, B:H.152, B:S.154, B:H.227, B:T.277, B:T.277, B:K.280, A:T.309, A:T.310, A:T.310 pi-Stacking: B:H.152 Water bridges: A:S.123

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: Y.16, E.17, I.20 Chain B: L.220, D.272, S.292, K.294, L.295 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:Y.16 Hydrogen bonds: B:D.272, B:D.272, B:S.292

1 x K: POTASSIUM ION(Non-covalent)

K.7: 4 residues within 4Å: Chain B: S.247, T.258, N.259, D.260 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.247, B:T.258, B:T.258, B:N.259, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, B.L. et al., Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme. Structure (2018)

Release Date

2018-03-28

Peptides

5-aminolevulinate synthase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

5-aminolevulinate synthase, mitochondrial

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