SMTL ID : 6qvg.1

Human SHMT2 in complex with lometrexol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

1 x GLY: GLYCINE(Non-covalent)

GLY.1: 8 residues within 4Å: Chain A: P.140, Y.141, R.286, S.287, H.328, H.330, A.331 Chain B: H.328 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.141, A:S.287 Salt bridges: A:H.328, A:H.330, B:H.328 Water bridges: B:H.328, B:H.328, B:H.328

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

PEG.2: 7 residues within 4Å: Chain A: R.66, R.69, E.401, L.402, S.404, R.486 Chain B: E.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69, A:S.404 Water bridges: A:R.66 PEG.3: 6 residues within 4Å: Chain A: D.65, C.68, R.494, F.496, P.497, M.498 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.65, A:R.494, A:M.498 Water bridges: B:Q.46

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: W.43, E.47, S.52 Chain B: Q.341 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.52, A:S.52 Water bridges: A:E.47, B:Q.341

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: A.394, K.409, I.419, T.420, P.421 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.420 GOL.6: 6 residues within 4Å: Chain A: P.145, L.148, L.323, Q.324 Chain B: P.145, Q.324 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.324, A:Q.324

2 x DDF: 5,10-DIDEAZATETRAHYDROFOLIC ACID(Non-covalent)

DDF.7: 14 residues within 4Å: Chain A: L.166, G.169, G.170, H.171, L.172, Y.176, K.181, I.183, S.226, R.425 Chain B: E.98, Y.105, F.317, P.321 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.172, A:Y.176, B:Y.105, B:Y.105, B:Y.105, B:P.321 Hydrogen bonds: A:G.170, A:G.170, A:L.172, A:S.226, A:R.425 Water bridges: A:N.408 Salt bridges: A:K.181 DDF.10: 13 residues within 4Å: Chain A: E.98, Y.105, F.317 Chain B: L.166, G.169, G.170, H.171, L.172, Y.176, K.181, I.183, S.226, R.425 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.172, B:Y.176, A:Y.105, A:Y.105 Hydrogen bonds: B:G.170, B:G.170, B:L.172, B:Y.176, B:S.226, B:R.425, B:R.425 Salt bridges: B:K.181

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.8: 18 residues within 4Å: Chain A: S.142, G.143, S.144, N.147, H.171, H.174, T.225, S.226, D.251, A.253, H.254, T.277, H.279, K.280 Chain B: Y.96, Y.141, G.325, G.326 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:K.280 Hydrogen bonds: A:G.143, A:S.144, A:S.144, A:N.147, A:T.225, B:Y.96, B:G.325, B:G.326 Water bridges: A:S.142, A:T.275, A:K.280, B:Y.141 Salt bridges: A:H.279, A:K.280 pi-Stacking: A:H.171 PLP.11: 18 residues within 4Å: Chain A: Y.96, Y.141, G.325, G.326 Chain B: S.142, G.143, S.144, N.147, H.171, H.174, T.225, S.226, D.251, A.253, H.254, T.277, H.279, K.280 17 PLIP interactions: 4 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:Y.96, A:Y.141, A:G.325, A:G.326, B:G.143, B:S.144, B:N.147, B:T.225 Hydrophobic interactions: B:H.171, B:A.253, B:K.280 Water bridges: B:S.142, B:T.275, B:K.280, B:R.286 Salt bridges: B:H.279 pi-Stacking: B:H.171

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain B: R.387, D.415, R.416, S.417, T.420 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.387 Hydrogen bonds: B:R.416, B:S.417

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scaletti, E. et al., Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs. Febs Lett. (2019)

Release Date

2019-09-04

Peptides

Serine hydroxymethyltransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine hydroxymethyltransferase, mitochondrial

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