SMTL ID : 6deb.1

Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase in the Complex with Methotrexate from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

1 x GUN: GUANINE(Non-covalent)

GUN.1: 8 residues within 4Å: Chain A: L.96, V.97, Q.98, L.99, D.121, F.123, T.143, I.171 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.97, A:L.99, A:D.121 Water bridges: A:K.54, A:K.54, A:D.121, A:T.143 Salt bridges: A:D.121 pi-Cation interactions: A:K.54

1 x K: POTASSIUM ION(Non-covalent)

K.2: 2 residues within 4Å: Chain A: M.4, T.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.4, A:T.5, H2O.8

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: L.145, M.148 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.149 GOL.5: 4 residues within 4Å: Chain A: I.166, H.191, I.192, A.211 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.191, A:I.192 GOL.6: 6 residues within 4Å: Chain A: A.168, R.174, H.191, K.193 Chain B: L.181, N.182 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.168, A:R.174, B:L.181 GOL.11: 2 residues within 4Å: Chain B: L.145, M.148 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.136 GOL.14: 3 residues within 4Å: Chain B: D.196, L.197, S.198 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.197, B:S.198, B:S.198 Water bridges: B:T.194

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

CL.4: 3 residues within 4Å: Chain A: P.261, G.262, P.266 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: I.233, P.261, G.262, G.265, P.266 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: H.191, I.192 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 10 residues within 4Å: Chain A: N.132, R.174, A.177, T.178, V.189 Chain B: N.132, R.174, A.177, T.178, V.189 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.132, B:T.178, A:N.132, A:N.132, A:T.178

2 x MTX: METHOTREXATE(Non-covalent)

MTX.8: 15 residues within 4Å: Chain B: L.96, V.97, Q.98, L.99, P.100, K.107, D.121, F.123, T.143, S.169, I.171, V.172, V.231, T.268 Ligands: MTX.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.171, B:V.172 Hydrogen bonds: B:V.97, B:L.99, B:L.99 Water bridges: B:D.121, B:T.143, B:S.169, B:I.171 Salt bridges: B:K.107, B:D.121 pi-Cation interactions: B:K.54 MTX.9: 10 residues within 4Å: Chain B: Y.50, K.54, Q.98, L.99, A.210, A.211, G.212, V.231, I.233 Ligands: MTX.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.50, B:I.233 Hydrogen bonds: B:Q.98 Water bridges: B:Y.50, B:I.233, B:N.234 Salt bridges: B:K.54

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.12: 8 residues within 4Å: Chain A: L.181, N.182, G.184 Chain B: A.168, R.174, H.191, I.192, K.193 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.182, B:R.174, B:K.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase in the Complex with Methotrexate from Campylobacter jejuni. To Be Published

Release Date

2018-05-23

Peptides

Bifunctional protein FolD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional protein FolD

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