SMTL ID : 6qvl.1

Human SHMT2 in complex with pemetrexed

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: K.200, T.201, G.202, L.372, V.373, S.374, G.375 Ligands: PEG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.374, A:S.374 Water bridges: A:P.199 GOL.2: 4 residues within 4Å: Chain A: R.219, K.245, A.246, H.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.219, A:R.219 GOL.6: 10 residues within 4Å: Chain B: A.223, G.224, T.225, I.232, Y.234, D.251, M.252, H.254, I.255 Ligands: PLP.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.223, B:T.225, B:T.225, B:H.254

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

PEG.3: 5 residues within 4Å: Chain A: T.201, L.203, R.230, S.374 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.230, A:D.378

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: K.262, I.264, P.265 No protein-ligand interaction detected (PLIP)

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

PLP.5: 16 residues within 4Å: Chain A: S.142, G.143, S.144, N.147, H.171, T.225, S.226, D.251, A.253, H.254, T.277, H.279, K.280 Chain B: Y.96, G.325, G.326 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:Y.96, B:G.325, B:G.326, A:G.143, A:S.144, A:S.144, A:N.147, A:H.254 Hydrophobic interactions: A:K.280 Water bridges: A:S.142, A:S.142, A:T.275 Salt bridges: A:H.279 pi-Stacking: A:H.171 PLP.8: 17 residues within 4Å: Chain A: Y.96, G.325, G.326 Chain B: S.142, G.143, S.144, N.147, H.171, T.225, S.226, D.251, A.253, H.254, T.277, H.279, K.280 Ligands: GOL.6 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.280 Hydrogen bonds: B:G.143, B:S.144, B:N.147, B:K.280, A:Y.96, A:G.325, A:G.326 Water bridges: B:S.76, B:S.142, B:T.277, B:R.286 Salt bridges: B:H.279, B:K.280 pi-Stacking: B:H.171

1 x 4DW: N-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}-L-glutamic acid(Non-covalent)

4DW.7: 11 residues within 4Å: Chain A: L.166, L.172, K.181, I.183, S.226, R.425 Chain B: E.98, Y.105, Y.106, F.317, P.321 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.166, A:L.172, B:Y.105, B:F.317, B:P.321, B:P.321 Hydrogen bonds: A:R.425, B:Y.106 Salt bridges: A:K.181

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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