SMTL ID : 4p3m.1

Crystal structure of serine hydroxymethyltransferase from Psychromonas ingrahamii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: I.33, A.34, S.35, L.318, N.345, R.363 Chain B: Y.65 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.65, A:A.34, A:S.35, A:S.35, A:N.345 Salt bridges: A:R.363 SO4.2: 8 residues within 4Å: Chain A: S.97, G.98, S.99, T.227, H.229 Chain B: Y.55, G.262, G.263 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.98, A:S.99, A:S.99, A:S.99, B:Y.55, B:Y.55, B:G.262, B:G.263 Water bridges: A:S.97, A:S.97 Salt bridges: A:H.229 SO4.3: 9 residues within 4Å: Chain A: Y.55, G.262, G.263 Chain B: S.97, G.98, S.99, T.227, H.229, K.230 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Y.55, A:G.262, A:G.263, B:G.98, B:S.99 Water bridges: B:S.97, B:S.97, B:R.236, B:R.236 Salt bridges: B:H.229, B:K.230 SO4.4: 3 residues within 4Å: Chain A: L.77, R.81, K.277 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.81, A:K.277 Salt bridges: A:R.81, A:K.277 SO4.12: 8 residues within 4Å: Chain A: Y.65 Chain B: I.33, A.34, S.35, H.204, L.318, N.345, R.363 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.34, B:S.35, B:H.204, A:Y.65 Salt bridges: B:R.363

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

CL.5: 8 residues within 4Å: Chain A: A.206, T.226, T.227, T.228, H.229, K.230, T.231, L.232 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: R.42 Chain B: M.6, N.7, D.10, Y.11 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: M.6, N.7, D.10, Y.11 Chain B: R.42 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: Y.59, P.60, I.79, Y.90, A.91, N.92, V.93, N.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.91, A:N.253 Water bridges: A:V.93 GOL.9: 5 residues within 4Å: Chain A: I.181, G.212, L.213, Y.214, P.215 No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain A: W.385, D.388, T.402, A.405, V.406, K.409 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.388, A:D.388, A:K.409 Water bridges: A:D.388 GOL.11: 5 residues within 4Å: Chain A: K.398, L.399, A.400, T.401, T.402 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.398, A:A.400, A:T.401, A:T.401 GOL.13: 13 residues within 4Å: Chain A: F.2, M.6 Chain B: T.39, S.40, L.232, G.233, G.234, A.275, E.278, C.279, F.284, Y.287, R.371 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.232, B:E.278, B:R.371 Water bridges: B:N.37, B:T.39, B:S.40 GOL.14: 7 residues within 4Å: Chain B: L.85, F.86, G.87, V.209, A.210, G.212, N.216 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.216 Water bridges: B:F.86, B:G.87, B:G.87, B:G.87 GOL.15: 8 residues within 4Å: Chain B: Y.59, P.60, I.79, Y.90, A.91, N.92, V.93, N.253 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.253 Water bridges: B:A.91, B:V.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Angelaccio, S. et al., Conformational transitions driven by pyridoxal-5'-phosphate uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii. Proteins (2014)

Release Date

2014-07-30

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase