SMTL ID : 3cl9.2 (2 other biounits)

Structure of bifunctional TcDHFR-TS in complex with MTX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.233, R.235 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.233, A:R.235 SO4.2: 7 residues within 4Å: Chain A: R.177, W.206, R.208, L.230 Chain B: R.249, E.250, G.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.177, A:W.206 Salt bridges: A:R.208 SO4.11: 2 residues within 4Å: Chain B: R.233, R.235 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.233, B:R.235 SO4.12: 7 residues within 4Å: Chain A: R.249, E.250, G.251 Chain B: R.177, W.206, R.208, L.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.177, B:W.206 Salt bridges: B:R.208

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

CL.3: 2 residues within 4Å: Chain A: R.78, K.79 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: R.53 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: E.336 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.78, K.79 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: R.53 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: E.336 Ligand excluded by PLIP

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.6: 27 residues within 4Å: Chain A: V.27, A.28, I.35, G.38, S.40, I.41, W.43, G.77, R.78, K.79, T.80, S.83, L.99, S.100, S.101, T.102, N.129, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: MTX.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.160 Hydrogen bonds: A:A.28, A:I.35, A:S.40, A:G.77, A:R.78, A:R.78, A:K.79, A:T.80, A:T.80, A:S.83, A:S.83, A:S.101, A:T.102, A:G.156, A:S.158, A:S.158, A:S.158 Salt bridges: A:R.78 NAP.16: 27 residues within 4Å: Chain B: V.27, A.28, I.35, G.38, S.40, I.41, W.43, G.77, R.78, K.79, T.80, S.83, L.99, S.100, S.101, T.102, N.129, G.130, G.131, I.154, G.155, G.156, G.157, S.158, V.159, Y.160 Ligands: MTX.17 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.160 Hydrogen bonds: B:A.28, B:I.35, B:S.40, B:G.77, B:R.78, B:R.78, B:K.79, B:T.80, B:S.83, B:S.83, B:S.101, B:T.102, B:G.156, B:S.158, B:S.158, B:S.158 Salt bridges: B:R.78

2 x MTX: METHOTREXATE(Non-covalent)

MTX.7: 20 residues within 4Å: Chain A: V.26, V.27, A.28, I.41, D.48, M.49, F.52, R.53, T.80, S.83, I.84, P.85, F.88, L.91, P.92, R.94, I.154, Y.160, T.178 Ligands: NAP.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.84, A:F.88, A:L.91 Hydrogen bonds: A:V.26, A:V.27, A:Y.160, A:T.178 Salt bridges: A:D.48, A:R.94 MTX.17: 20 residues within 4Å: Chain B: V.26, V.27, A.28, I.41, D.48, M.49, F.52, R.53, T.80, S.83, I.84, P.85, F.88, L.91, P.92, R.94, I.154, Y.160, T.178 Ligands: NAP.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.84, B:F.88, B:L.91 Hydrogen bonds: B:V.26, B:V.27, B:Y.160 Salt bridges: B:D.48, B:R.94

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.8: 12 residues within 4Å: Chain A: R.257, C.403, H.404, Q.422, R.423, S.424, C.425, D.426, G.430, N.434, H.464, Y.466 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.426 Hydrogen bonds: A:S.424, A:D.426, A:N.434, A:N.434, A:H.464, A:Y.466 Salt bridges: A:R.423 UMP.18: 12 residues within 4Å: Chain B: R.257, C.403, H.404, Q.422, R.423, S.424, C.425, D.426, G.430, N.434, H.464, Y.466 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.426 Hydrogen bonds: B:S.424, B:D.426, B:N.434, B:N.434, B:H.464 Salt bridges: B:R.423

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: F.51, T.210, F.227 No protein-ligand interaction detected (PLIP) EDO.10: 1 residues within 4Å: Chain A: R.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.60 EDO.19: 3 residues within 4Å: Chain B: F.51, T.210, F.227 No protein-ligand interaction detected (PLIP) EDO.20: 1 residues within 4Å: Chain B: R.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function. Proteins (2008)

Release Date

2009-01-06

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS)

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