SMTL ID : 4oyt.1 (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 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.34, A:S.100, A:S.100, A:G.101, A:S.102, A:N.105, A:S.210, B:E.56, B:E.56, B:G.271, B:G.272 Water bridges: A:S.100, A:S.102, A:S.102, A:R.243 Salt bridges: A:H.211, A:H.236, 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 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.34, B:G.101, B:S.102, B:N.105, B:S.210, A:Y.54, A:E.56, A:Y.64, A:G.271, A:G.272 Water bridges: B:S.100, B:H.129, 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: 15 residues within 4Å: Chain A: L.124, G.127, G.128, H.129, L.130, F.134, V.141, T.183, C.364 Chain B: E.56, Y.63, Y.64, P.267 Ligands: 1W9.1, GOL.4 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Y.64, A:G.128, A:L.130 pi-Stacking: B:Y.63 Hydrophobic interactions: A:L.124, A:L.130 Water bridges: A:N.354, A:N.354, A:N.356 FON.6: 14 residues within 4Å: Chain A: E.56, Y.63, Y.64, P.267 Chain B: L.124, G.127, G.128, H.129, L.130, K.139, V.141, T.183, S.184 Ligands: 1W9.5 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.130, A:Y.63 Hydrogen bonds: B:G.127, B:L.130, B:T.183, B:S.184, A:E.56 Water bridges: B:K.355, B:N.356

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: S.126, C.155, G.159, S.184, Y.185, P.186, V.319, V.329, T.357, I.358, P.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.356, A:T.357 GOL.4: 5 residues within 4Å: Chain A: K.355, N.356, T.357, C.364 Ligands: FON.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.355, A:T.357 Water bridges: A:C.125, A:N.354, A:N.354, A:N.356 GOL.7: 6 residues within 4Å: Chain A: A.103 Chain B: L.99, A.103, Q.107, F.269, Q.270 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.107, B:S.100

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
A

B
B

Serine hydroxymethyltransferase, putative

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