SMTL ID : 1f3f.1

STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: R.92 Ligands: D4T.2 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Ligands: PO4.3, D4T.5, D4D.6 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: D4T.8 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain D: R.92 Ligands: D4T.10 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Ligands: PO4.11, D4T.13, D4D.14 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: D4T.16 No protein-ligand interaction detected (PLIP)

6 x D4T: 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE(Non-covalent)

D4T.2: 14 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, G.122, G.123 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.64, A:V.116 Hydrogen bonds: A:Y.56, A:Y.56, A:G.123 Water bridges: A:R.92, A:R.92, A:T.98 Salt bridges: A:K.16, A:H.59, A:R.92, A:R.92, A:R.109, A:R.109 pi-Stacking: A:F.64 D4T.5: 16 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, G.122, G.123 Ligands: PO4.3, MG.4, D4D.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.64, B:V.116 Hydrogen bonds: B:Y.56, B:G.123 Water bridges: B:Y.56, B:T.98 Salt bridges: B:K.16, B:H.59, B:R.92, B:R.92, B:R.109, B:R.109 pi-Stacking: B:F.64 D4T.8: 14 residues within 4Å: Chain C: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119, G.122, G.123 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.64, C:T.98, C:V.116 Hydrogen bonds: C:Y.56, C:Y.56, C:G.123 Salt bridges: C:K.16, C:H.59, C:R.92, C:R.92, C:R.109, C:R.109 pi-Stacking: C:F.64 D4T.10: 14 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, G.122, G.123 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.64, D:V.116 Hydrogen bonds: D:Y.56, D:G.123 Water bridges: D:R.92, D:R.92 Salt bridges: D:K.16, D:H.59, D:R.92, D:R.92, D:R.109, D:R.109 pi-Stacking: D:F.64 D4T.13: 16 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, G.122, G.123 Ligands: PO4.11, MG.12, D4D.14 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.64, E:V.116 Hydrogen bonds: E:G.123 Water bridges: E:Y.56 Salt bridges: E:K.16, E:H.59, E:R.92, E:R.92, E:R.109, E:R.109 pi-Stacking: E:F.64 D4T.16: 14 residues within 4Å: Chain F: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119, G.122, G.123 Ligands: MG.15 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.64, F:T.98, F:V.116 Hydrogen bonds: F:Y.56, F:G.123 Salt bridges: F:K.16, F:H.59, F:R.92, F:R.92, F:R.109, F:R.109 pi-Stacking: F:F.64

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain B: K.16, H.55, Y.56, R.92, G.122, G.123 Ligands: MG.4, D4T.5, D4D.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.56, B:G.123 Water bridges: B:E.58 Salt bridges: B:K.16, B:R.92 PO4.11: 9 residues within 4Å: Chain E: K.16, H.55, Y.56, R.92, G.122, G.123 Ligands: MG.12, D4T.13, D4D.14 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.123 Salt bridges: E:K.16, E:R.92

2 x D4D: 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE(Non-covalent)

D4D.6: 15 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 Chain C: E.155 Ligands: PO4.3, MG.4, D4T.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.64, B:V.116 Hydrogen bonds: B:T.98 Water bridges: B:T.98 Salt bridges: B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64 D4D.14: 15 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 Chain F: E.155 Ligands: PO4.11, MG.12, D4T.13 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.64, E:V.116 Water bridges: E:T.98 Salt bridges: E:H.59, E:R.92, E:R.109 pi-Stacking: E: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)

Related Entries With Identical Sequence