SMTL ID : 5tc4.1

Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 21 residues within 4Å: Chain A: T.142, G.166, R.167, S.168, N.170, V.171, H.198, R.199, A.219, A.220, G.221, I.222, L.225, V.240, G.241, I.242, V.278, G.279, T.282 Ligands: L34.2, PO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.142, A:V.171, A:V.240, A:I.242 Hydrogen bonds: A:R.167, A:S.168, A:S.168, A:N.170, A:R.199, A:R.199, A:V.240, A:I.242, A:N.243 Water bridges: A:S.168, A:S.168, A:R.199, A:T.201 NAD.4: 21 residues within 4Å: Chain B: T.142, G.166, R.167, S.168, N.170, V.171, H.198, R.199, A.219, A.220, G.221, I.222, L.225, V.240, G.241, I.242, V.278, G.279, T.282 Ligands: L34.5, PO4.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.142, B:V.171, B:V.240, B:I.242 Hydrogen bonds: B:R.167, B:S.168, B:S.168, B:N.170, B:R.199, B:R.199, B:V.240, B:I.242, B:N.243 Water bridges: B:S.168, B:S.168, B:R.199, B:T.201

2 x L34: 4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID(Non-covalent)

L34.2: 18 residues within 4Å: Chain A: Y.50, N.53, K.54, V.97, Q.98, L.99, D.121, F.123, I.242, R.244, L.255, P.275, G.276, G.279, P.280, T.282, V.283 Ligands: NAD.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.50, A:I.242, A:L.255, A:T.282, A:V.283 Hydrogen bonds: A:N.53, A:K.54, A:V.97, A:Q.98, A:L.99, A:L.99, A:G.276 Water bridges: A:Y.50, A:K.54, A:A.141, A:G.277, A:G.279 Salt bridges: A:D.121, A:R.244 pi-Stacking: A:Y.50 pi-Cation interactions: A:K.54 L34.5: 18 residues within 4Å: Chain B: Y.50, N.53, K.54, V.97, Q.98, L.99, D.121, F.123, I.242, R.244, L.255, P.275, G.276, G.279, P.280, T.282, V.283 Ligands: NAD.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.50, B:I.242, B:L.255, B:T.282, B:V.283 Hydrogen bonds: B:N.53, B:K.54, B:V.97, B:Q.98, B:L.99, B:L.99, B:G.276 Water bridges: B:Y.50, B:K.54, B:A.141, B:G.277, B:G.279 Salt bridges: B:D.121, B:R.244 pi-Stacking: B:Y.50 pi-Cation interactions: B:K.54

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: R.167, R.199 Chain B: D.182, H.185 Ligands: NAD.1 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.167, A:R.199, B:H.185 Hydrogen bonds: B:D.182, B:D.182 Water bridges: B:D.182 PO4.6: 5 residues within 4Å: Chain A: D.182, H.185 Chain B: R.167, R.199 Ligands: NAD.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.167, B:R.199, A:H.185 Hydrogen bonds: A:D.182, A:D.182 Water bridges: A:D.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gustafsson, R. et al., Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor. Cancer Res. (2017)

Release Date

2016-12-14

Peptides

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

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