SMTL ID : 7th4.1

T. thermophilus methylenetetrahydrofolate reductase complex with 5-formyltetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: E.18, T.49, Y.50, A.52, H.77, T.79, L.104, L.106, R.107, G.108, D.109, P.110, Y.126, A.127, A.128, A.147, A.148, Y.149, H.153, E.155, S.156, D.162, H.165, A.168, K.169, I.178, T.179, Q.180, H.270, Y.272 Ligands: FFO.2 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:A.147, A:I.178 Hydrogen bonds: A:Y.50, A:Y.50, A:H.77, A:R.107, A:R.107, A:G.108, A:D.109, A:D.109, A:A.127, A:Y.149, A:Y.149, A:Y.149, A:H.153, A:S.156, A:H.165 Water bridges: A:A.52, A:A.52, A:R.107, A:D.109, A:D.109, A:Y.126, A:Y.126, A:A.128, A:A.147, A:E.155, A:E.155, A:K.169, A:K.169, A:Q.180 Salt bridges: A:R.107, A:H.153, A:H.153, A:K.169, A:K.169 pi-Stacking: A:H.165, A:H.165 FAD.5: 29 residues within 4Å: Chain B: E.18, T.49, Y.50, A.52, H.77, T.79, L.104, L.106, R.107, G.108, D.109, P.110, Y.126, A.127, A.147, A.148, Y.149, H.153, E.155, S.156, D.162, H.165, K.169, I.178, T.179, Q.180, H.270, Y.272 Ligands: FFO.6 39 PLIP interactions: 39 interactions with chain B Hydrophobic interactions: B:L.104, B:A.147, B:I.178 Hydrogen bonds: B:Y.50, B:Y.50, B:H.77, B:R.107, B:R.107, B:G.108, B:D.109, B:A.127, B:Y.149, B:Y.149, B:Y.149, B:H.153, B:S.156, B:D.162, B:H.165 Water bridges: B:A.52, B:R.107, B:D.109, B:D.109, B:D.109, B:Y.126, B:Y.126, B:A.128, B:A.147, B:K.169, B:K.169, B:Q.180 Salt bridges: B:R.107, B:H.153, B:H.153, B:K.169, B:K.169 pi-Stacking: B:Y.126, B:Y.126, B:H.165, B:H.165

2 x FFO: N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid(Non-covalent)

FFO.2: 18 residues within 4Å: Chain A: E.18, F.20, K.23, T.49, D.109, Y.149, Q.180, L.181, M.209, R.215, Q.216, R.219, F.220, V.223, C.224, Y.272, L.274 Ligands: FAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.20, A:F.220 Hydrogen bonds: A:Q.180, A:Q.180, A:Q.216, A:R.219, A:V.223 Salt bridges: A:K.23, A:D.109, A:R.219 FFO.6: 18 residues within 4Å: Chain B: E.18, F.20, K.23, T.49, D.109, Y.149, Q.180, L.181, M.209, R.215, Q.216, R.219, F.220, V.223, C.224, Y.272, L.274 Ligands: FAD.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.20 Hydrogen bonds: B:Q.180, B:Q.180, B:Q.216, B:R.219, B:V.223 Water bridges: B:D.109, B:D.109, B:D.109 Salt bridges: B:K.23, B:D.109, B:R.219

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

CL.3: 6 residues within 4Å: Chain A: A.147, A.148, Y.149, H.153, F.166, K.169 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: H.93, E.97, R.137, Y.138, R.141 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: A.147, A.148, Y.149, H.153, F.166, K.169 Ligand excluded by PLIP

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

ACT.4: 12 residues within 4Å: Chain B: V.46, S.47, I.48, S.60, W.63, A.64, I.67, P.74, L.75, A.76, H.77, F.95 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.64, B:I.67 Hydrogen bonds: B:I.48, B:S.60, B:H.77 Water bridges: B:S.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, K. et al., 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity. J.Biol.Chem. (2022)

Release Date

2023-01-18

Peptides

Methylenetetrahydrofolate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methylenetetrahydrofolate reductase

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