SMTL ID : 1f6t.1

STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.92 Ligands: TBD.2 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: R.92 Ligands: TBD.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: E.58, R.92 Ligands: TBD.6 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain D: R.92 Ligands: TBD.8 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: R.92 Ligands: TBD.10 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain F: E.58, R.92 Ligands: TBD.12 No protein-ligand interaction detected (PLIP)

6 x TBD: 2*-DEOXY-THYMIDINE-5*-ALPHA BORANO DIPHOSPHATE (ISOMER RP)(Non-covalent)

TBD.2: 12 residues within 4Å: Chain A: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.64 Hydrogen bonds: A:K.16, A:R.109, A:N.119 Water bridges: A:K.16, A:Y.56, A:R.92, A:R.92, A:R.92, A:R.92, A:R.109, A:H.122 Salt bridges: A:R.92, A:R.109 pi-Stacking: A:F.64 TBD.4: 12 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.64, B:V.116 Hydrogen bonds: B:K.16, B:R.109, B:N.119 Water bridges: B:K.16, B:Y.56, B:R.92, B:R.92, B:R.92, B:R.92, B:H.122 Salt bridges: B:R.92, B:R.109 pi-Stacking: B:F.64 TBD.6: 12 residues within 4Å: Chain A: E.155 Chain C: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.64 Hydrogen bonds: C:K.16, C:R.109, C:N.119 Water bridges: C:E.58, C:R.92, C:R.92, C:R.109, C:I.121, C:H.122, C:H.122 Salt bridges: C:R.92, C:R.109 pi-Stacking: C:F.64 TBD.8: 12 residues within 4Å: Chain D: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.64 Hydrogen bonds: D:K.16, D:R.109, D:N.119 Water bridges: D:K.16, D:R.92, D:R.92, D:R.92, D:R.92, D:T.98, D:T.98, D:T.98, D:T.98 Salt bridges: D:R.92, D:R.109 pi-Stacking: D:F.64 TBD.10: 12 residues within 4Å: Chain E: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.9 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.64, E:V.116 Hydrogen bonds: E:K.16, E:R.109, E:N.119 Water bridges: E:K.16, E:R.92, E:R.92, E:R.92, E:R.92, E:H.122, E:H.122 Salt bridges: E:R.92, E:R.109 pi-Stacking: E:F.64 TBD.12: 12 residues within 4Å: Chain D: E.155 Chain F: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:F.64 Hydrogen bonds: F:K.16, F:R.109, F:N.119 Water bridges: F:R.92, F:R.92, F:R.109, F:I.121, F:H.122, F:H.122, F:H.122, F:H.122, F:G.123 Salt bridges: F:R.92, F:R.109 pi-Stacking: F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, P. et al., Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase. EMBO J. (2000)

Release Date

2000-09-13

Peptides

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)

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