SMTL ID : 6yme.1

Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-internal aldimine state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: I.54, S.56, H.147, S.197, H.225, K.251, R.383 Chain B: Y.76, E.78, Y.86 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.56, A:R.383, A:R.383, B:Y.86 Water bridges: B:Y.86 GOL.2: 6 residues within 4Å: Chain A: E.171, T.172, E.173, K.328, S.331, G.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.173, A:K.328, A:S.331 GOL.3: 3 residues within 4Å: Chain A: Q.321, R.325, N.404 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.321 Water bridges: A:R.325, A:R.325, A:R.325, A:R.325 GOL.4: 2 residues within 4Å: Chain A: S.232, G.233 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.106, A:K.305 GOL.5: 7 residues within 4Å: Chain A: P.62, T.391, R.392, P.434, L.435, Y.436, P.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.392, A:Y.436 GOL.7: 10 residues within 4Å: Chain A: Y.76, E.78, Y.86 Chain B: I.54, S.56, H.147, S.197, H.225, K.251, R.383 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.78, A:Y.86, A:Y.86, B:S.56, B:R.383, B:R.383 GOL.8: 6 residues within 4Å: Chain B: E.171, T.172, E.173, K.328, S.331, G.332 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.173, B:E.173, B:K.328, B:S.331 GOL.9: 3 residues within 4Å: Chain B: Q.321, R.325, N.404 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.321 Water bridges: B:R.325, B:R.325, B:R.325, B:R.325 GOL.10: 2 residues within 4Å: Chain B: S.232, G.233 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.106, B:K.305 GOL.11: 7 residues within 4Å: Chain B: P.62, T.391, R.392, P.434, L.435, Y.436, P.437 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.392, B:Y.436

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

PEG.6: 4 residues within 4Å: Chain A: T.129, Y.218, L.268, K.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.218, A:K.271 PEG.12: 4 residues within 4Å: Chain B: T.129, Y.218, L.268, K.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.271

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
A

Serine hydroxymethyltransferase

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