SMTL ID : 2f64.1

Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6 A resolution with 1-METHYLQUINOLIN-2(1H)-ONE bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.6, H.7, H.8, M.9, K.11 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.11, A:K.11 Salt bridges: A:H.6, A:H.8, A:K.11 SO4.4: 5 residues within 4Å: Chain B: H.6, H.7, H.8, M.9, K.11 7 PLIP interactions: 7 interactions with chain B Water bridges: B:H.8, B:K.11, B:K.11, B:K.11 Salt bridges: B:H.6, B:H.8, B:K.11

2 x 12Q: 1-METHYLQUINOLIN-2(1H)-ONE(Non-covalent)

12Q.2: 12 residues within 4Å: Chain A: V.19, F.20, P.46, T.47, E.50, I.57, N.61 Chain B: E.127, N.134, L.135, M.136 Ligands: GOL.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.19, A:P.46, A:T.47, A:E.50, A:I.57, B:L.135 Hydrogen bonds: B:N.134 12Q.5: 12 residues within 4Å: Chain A: E.127, N.134, L.135, M.136 Chain B: V.19, F.20, P.46, T.47, E.50, I.57, N.61 Ligands: GOL.6 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.135, B:V.19, B:P.46, B:T.47, B:E.50, B:I.57 Hydrogen bonds: A:N.134, A:L.135

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: A.15, G.16, V.19, F.20, P.46, D.84, G.86, T.87, E.90 Chain B: N.134 Ligands: 12Q.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.16, A:D.84, A:G.86, A:T.87, A:T.87, B:N.134 GOL.6: 11 residues within 4Å: Chain A: N.134 Chain B: A.15, G.16, V.19, F.20, P.46, D.84, G.86, T.87, E.90 Ligands: 12Q.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.16, B:D.84, B:G.86, B:T.87, B:T.87, A:N.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bosch, J. et al., Using fragment cocktail crystallography to assist inhibitor design of Trypanosoma brucei nucleoside 2-deoxyribosyltransferase. J.Med.Chem. (2006)

Release Date

2005-12-06

Peptides

Nucleoside 2-deoxyribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nucleoside 2-deoxyribosyltransferase

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