SMTL ID : 6ymf.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: F.59, S.61, P.62, T.391, L.435, Y.436, P.437 Ligands: GOL.2 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: S.61, R.254, E.298 Ligands: GOL.1 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: Q.321, R.325, N.404 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: A.231, S.232, G.233, K.305 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: G.79, L.80, K.274, F.277 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: R.188, P.189, K.190, V.215, G.216 Ligand excluded by PLIP GOL.9: 3 residues within 4Å: Chain A: G.216, A.217, Y.218 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: Y.177, D.178, A.210 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain B: F.59, S.61, P.62, T.391, L.435, Y.436, P.437 Ligands: GOL.12 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: S.61, R.254, E.298 Ligands: GOL.11 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain B: Q.321, R.325, N.404 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: A.231, S.232, G.233, K.305 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: G.79, L.80, K.274, F.277 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: R.188, P.189, K.190, V.215, G.216 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: G.216, A.217, Y.218 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: Y.177, D.178, A.210 Ligand excluded by PLIP

2 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)

PLS.4: 19 residues within 4Å: Chain A: S.56, S.118, G.119, A.120, H.147, Y.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251, R.383 Chain B: Y.76, E.78, Y.86, G.282, G.283 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.224 Hydrogen bonds: A:S.56, A:G.119, A:A.120, A:S.197, A:K.251, B:Y.76, B:E.78, B:Y.86, B:Y.86, B:G.282, B:G.283 Water bridges: A:S.118, A:S.118, A:T.246, A:R.257 Salt bridges: A:H.225, A:H.250, A:K.251, A:R.383 pi-Stacking: A:H.147 PLS.14: 19 residues within 4Å: Chain A: Y.76, E.78, Y.86, G.282, G.283 Chain B: S.56, S.118, G.119, A.120, H.147, Y.196, S.197, D.222, A.224, H.225, T.248, H.250, K.251, R.383 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:A.224 Hydrogen bonds: B:S.56, B:G.119, B:A.120, B:S.197, B:K.251, A:Y.76, A:Y.76, A:E.78, A:Y.86, A:Y.86, A:G.282, A:G.283 Water bridges: B:S.118, B:S.118, B:N.123, B:R.257 Salt bridges: B:H.225, B:H.250, B:K.251, B:R.383 pi-Stacking: B:H.147

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 5 residues within 4Å: Chain A: T.129, Y.218, E.267, L.268, K.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.218, A:K.271 1PE.16: 5 residues within 4Å: Chain B: T.129, Y.218, E.267, 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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