SMTL ID : 2c7v.1

Structure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, A.96, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: MTX.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:P.204 Hydrogen bonds: A:R.14, A:I.15, A:H.35, A:N.36, A:N.36, A:S.37, A:D.62, A:L.63, A:T.64, A:T.64, A:N.93, A:S.95, A:S.95, A:S.95, A:Y.174, A:K.178, A:S.207, A:L.208 Water bridges: A:R.14, A:G.16, A:H.35, A:H.35, A:S.37, A:S.37, A:N.93, A:S.95 Salt bridges: A:R.14, A:R.14 pi-Stacking: A:H.35 NAP.5: 28 residues within 4Å: Chain B: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, A.96, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: MTX.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.204 Hydrogen bonds: B:R.14, B:I.15, B:H.35, B:H.35, B:N.36, B:N.36, B:S.37, B:D.62, B:D.62, B:L.63, B:T.64, B:T.64, B:N.93, B:S.95, B:S.95, B:S.95, B:Y.174, B:K.178, B:S.207, B:L.208 Water bridges: B:R.14, B:G.16, B:N.93, B:S.95 Salt bridges: B:R.14, B:R.14 pi-Stacking: B:H.35 NAP.9: 27 residues within 4Å: Chain C: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: MTX.10 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:P.204 Hydrogen bonds: C:R.14, C:I.15, C:H.35, C:N.36, C:N.36, C:S.37, C:D.62, C:L.63, C:N.93, C:S.95, C:S.95, C:S.95, C:K.178, C:S.207, C:L.208 Water bridges: C:A.12, C:A.12, C:R.14, C:G.16, C:N.93, C:S.95 Salt bridges: C:R.14, C:R.14 pi-Stacking: C:H.35 NAP.11: 27 residues within 4Å: Chain D: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: MTX.12 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.204 Hydrogen bonds: D:R.14, D:I.15, D:H.35, D:N.36, D:N.36, D:S.37, D:D.62, D:D.62, D:L.63, D:T.64, D:N.93, D:S.95, D:S.95, D:S.95, D:K.178, D:G.205, D:S.207 Water bridges: D:R.14, D:G.16, D:N.93, D:S.95 Salt bridges: D:R.14, D:R.14 pi-Stacking: D:H.35

4 x MTX: METHOTREXATE(Non-covalent)

MTX.2: 13 residues within 4Å: Chain A: R.14, S.95, F.97, P.99, C.168, F.171, Y.174, G.205, L.208, P.210, M.213, W.221 Ligands: NAP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.97, A:F.97, A:P.210, A:W.221 Hydrogen bonds: A:R.14, A:S.95, A:S.95, A:Y.174, A:Y.174 Water bridges: A:G.214 pi-Stacking: A:F.97, A:F.97 MTX.6: 16 residues within 4Å: Chain B: R.14, S.95, F.97, P.99, D.161, C.168, F.171, Y.174, G.205, L.208, L.209, P.210, M.213, E.217, W.221 Ligands: NAP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.97, B:P.210, B:W.221 Hydrogen bonds: B:R.14, B:S.95, B:S.95, B:Y.174, B:Y.174, B:E.217 pi-Stacking: B:F.97, B:F.97 MTX.10: 16 residues within 4Å: Chain C: R.14, S.95, F.97, P.99, D.161, C.168, F.171, Y.174, G.205, L.208, L.209, P.210, M.213, E.217, W.221 Ligands: NAP.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.97, C:P.210, C:W.221 Hydrogen bonds: C:R.14, C:S.95, C:S.95, C:Y.174, C:E.217 Water bridges: C:G.214 pi-Stacking: C:F.97, C:F.97 MTX.12: 14 residues within 4Å: Chain D: R.14, S.95, F.97, P.99, D.161, C.168, F.171, Y.174, G.205, L.208, P.210, M.213, W.221 Ligands: NAP.11 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.97, D:P.210, D:W.221 Hydrogen bonds: D:R.14, D:S.95, D:S.95, D:Y.174 Water bridges: D:K.220 pi-Stacking: D:F.97, D:F.97

2 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 2 residues within 4Å: Chain A: H.179 Chain C: H.179 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.179, C:H.179 NI.7: 2 residues within 4Å: Chain B: H.179 Chain D: H.179 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Metal complexes: B:H.179, D:H.179

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

ACT.4: 3 residues within 4Å: Chain A: E.215, K.218, R.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.218 Salt bridges: A:K.218, A:R.222 ACT.8: 4 residues within 4Å: Chain B: A.212, M.213, G.214, E.215 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.215 Hydrogen bonds: B:A.212 Water bridges: B:K.218 Salt bridges: B:K.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition by the Archetypal Antifolate Methotrexate. Mol.Microbiol. (2006)

Release Date

2006-09-19

Peptides

PTERIDINE REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PTERIDINE REDUCTASE

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