SMTL ID : 6ymd.1

Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Covalent)

PMP.1: 16 residues within 4Å: Chain A: S.118, G.119, A.120, H.147, Y.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251 Chain B: Y.76, G.282, G.283 Ligands: MLI.6 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.224, A:K.251 Hydrogen bonds: A:G.119, A:A.120, A:Y.196, B:Y.76, B:G.282, B:G.283 Water bridges: A:S.118, A:S.118, A:T.246 Salt bridges: A:H.250 pi-Stacking: A:H.147 PMP.7: 16 residues within 4Å: Chain A: Y.76, G.282, G.283 Chain B: S.118, G.119, A.120, H.147, Y.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251 Ligands: MLI.4 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:K.251 Hydrogen bonds: B:G.119, B:A.120, B:Y.196, A:Y.76, A:Y.76, A:G.282, A:G.283 Water bridges: B:S.118, B:S.118, B:N.123 Salt bridges: B:H.250 pi-Stacking: B:H.147

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: P.62, L.435, Y.436 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.436 EDO.3: 2 residues within 4Å: Chain A: P.153, H.165 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain B: Q.41, K.42, Q.45, N.440 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.440 Water bridges: B:G.38, B:Q.41, B:Q.45 EDO.9: 4 residues within 4Å: Chain B: R.188, K.190, V.215, G.216 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.215 EDO.10: 6 residues within 4Å: Chain B: L.106, F.107, V.230, A.231, G.233, N.237 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.107

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

MLI.4: 10 residues within 4Å: Chain A: Y.76, E.78, Y.86 Chain B: S.56, H.147, S.197, H.225, K.251, R.383 Ligands: PMP.7 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.56, B:S.197, A:Y.86, A:Y.86 Water bridges: B:S.197, B:S.197, B:R.383 Salt bridges: B:H.147, B:H.225, B:K.251, B:K.251, B:R.383 MLI.6: 10 residues within 4Å: Chain A: S.56, H.147, S.197, H.225, K.251, R.383 Chain B: Y.76, E.78, Y.86 Ligands: PMP.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.56, A:S.197, B:Y.86 Water bridges: A:S.197, A:S.197 Salt bridges: A:H.147, A:H.225, A:K.251, A:K.251, A:R.383

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: L.343, V.346, L.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.348, A:L.348 NA.11: 3 residues within 4Å: Chain B: G.158, F.161, E.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogues, I. et al., Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance. Int.J.Biol.Macromol. (2020)

Release Date

2020-06-03

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase

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