SMTL ID : 4oyt.2 (1 other biounit)

Crystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 1W9: (2R)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanyl-propanoic acid(Non-covalent)

1W9.1: 21 residues within 4Å: Chain A: S.34, S.100, G.101, S.102, N.105, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 Chain B: Y.54, E.56, Y.64, G.271, G.272 Ligands: FON.2 21 PLIP interactions: 5 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:E.56, B:E.56, B:G.271, B:G.272, A:S.34, A:S.100, A:G.101, A:S.102, A:N.105, A:S.210, A:K.237 Water bridges: B:H.274, A:S.100, A:T.232, A:H.236 Salt bridges: A:H.211, A:H.236, A:K.237, A:K.237, A:R.371 pi-Stacking: A:H.129 1W9.5: 21 residues within 4Å: Chain A: Y.54, E.56, Y.64, G.271, G.272 Chain B: S.34, S.100, G.101, S.102, N.105, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 Ligands: FON.6 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:S.34, B:S.100, B:G.101, B:S.102, B:N.105, B:S.210, B:K.237, A:Y.54, A:E.56, A:E.56, A:E.56, A:Y.64, A:G.271, A:G.272 Water bridges: B:S.100, B:R.243, A:Y.54 Salt bridges: B:H.211, B:H.236, B:K.237, B:K.237, B:R.371 pi-Stacking: B:H.129

2 x FON: N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid(Non-covalent)

FON.2: 14 residues within 4Å: Chain A: L.124, G.127, G.128, H.129, L.130, F.134, K.139, V.141, T.183, S.184 Chain B: E.56, Y.63, Y.64 Ligands: 1W9.1 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.63, B:Y.64, A:G.127, A:L.130 pi-Stacking: B:Y.63 Hydrophobic interactions: A:L.124, A:L.130 FON.6: 14 residues within 4Å: Chain A: E.56, Y.63, Y.64 Chain B: L.124, G.127, G.128, H.129, L.130, F.134, K.139, V.141, T.183, S.184 Ligands: 1W9.5 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.124, B:L.130 Hydrogen bonds: B:G.127, B:L.130, B:T.183, A:E.56, A:Y.63 pi-Stacking: A:Y.63

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 13 residues within 4Å: Chain A: C.125, S.126, G.127, C.155, G.159, S.184, Y.185, P.186, V.319, V.329, N.356, T.357, I.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.126, A:G.159, A:N.356, A:N.356 TRS.7: 13 residues within 4Å: Chain B: C.125, S.126, G.127, C.155, G.159, S.184, Y.185, P.186, V.319, V.329, N.356, T.357, I.358 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.126, B:G.159, B:N.356, B:N.356

2 x ETF: TRIFLUOROETHANOL(Non-covalent)

ETF.4: 6 residues within 4Å: Chain A: Q.78, G.93, V.94, F.249, E.258, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.258, A:N.262 ETF.8: 6 residues within 4Å: Chain B: Q.78, G.93, V.94, F.249, E.258, N.262 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chitnumsub, P. et al., Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-12-10

Peptides

Serine hydroxymethyltransferase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Serine hydroxymethyltransferase, putative

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