SMTL ID : 1b4s.1

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: K.16, H.55, Y.56, R.92, R.109, G.122, G.123 Ligands: MG.2, ADP.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.55, A:Y.56, A:Y.56, A:R.109, A:G.123, A:G.123 Salt bridges: A:K.16, A:R.92 PO4.4: 9 residues within 4Å: Chain B: K.16, H.55, Y.56, R.92, R.109, G.122, G.123 Ligands: MG.5, ADP.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.56, B:R.109, B:G.123, B:G.123 Water bridges: B:E.58 Salt bridges: B:K.16, B:R.92 PO4.7: 9 residues within 4Å: Chain C: K.16, H.55, Y.56, R.92, R.109, G.122, G.123 Ligands: MG.8, ADP.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.56, C:Y.56, C:Y.56, C:R.92, C:R.109, C:G.123, C:G.123 Salt bridges: C:K.16, C:H.55 PO4.10: 9 residues within 4Å: Chain D: K.16, H.55, Y.56, R.92, R.109, G.122, G.123 Ligands: MG.11, ADP.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.55, D:Y.56, D:R.109, D:G.123, D:G.123 Salt bridges: D:K.16, D:R.92 PO4.13: 9 residues within 4Å: Chain E: K.16, H.55, Y.56, R.92, R.109, G.122, G.123 Ligands: MG.14, ADP.15 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.109, E:G.123, E:G.123 Salt bridges: E:K.16, E:R.92 PO4.16: 9 residues within 4Å: Chain F: K.16, H.55, Y.56, R.92, R.109, G.122, G.123 Ligands: MG.17, ADP.18 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:Y.56, F:Y.56, F:R.92, F:R.109, F:G.123, F:G.123 Salt bridges: F:K.16, F:H.55

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.58, D.125 Ligands: PO4.1, ADP.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: E.58 Ligands: PO4.4, ADP.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain C: E.58, D.125 Ligands: PO4.7, ADP.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: E.58, D.125 Ligands: PO4.10, ADP.12 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain E: E.58 Ligands: PO4.13, ADP.15 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain F: E.58, D.125 Ligands: PO4.16, ADP.18 No protein-ligand interaction detected (PLIP)

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 12 residues within 4Å: Chain A: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: PO4.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.16, A:N.119, A:N.119 Salt bridges: A:H.59, A:R.92, A:R.109 pi-Stacking: A:F.64, A:F.64 ADP.6: 13 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Chain C: E.155 Ligands: PO4.4, MG.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.16, B:R.109, B:N.119, B:N.119 Salt bridges: B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64 ADP.9: 14 residues within 4Å: Chain A: E.155 Chain C: K.16, Y.56, H.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: PO4.7, MG.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.16, C:R.62, C:N.119, C:N.119 Salt bridges: C:H.59, C:R.92, C:R.109 pi-Stacking: C:F.64, C:F.64 ADP.12: 12 residues within 4Å: Chain D: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: PO4.10, MG.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.16, D:N.119, D:N.119 Salt bridges: D:H.59, D:R.92, D:R.109 pi-Stacking: D:F.64, D:F.64 ADP.15: 13 residues within 4Å: Chain E: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Chain F: E.155 Ligands: PO4.13, MG.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:K.16, E:R.109, E:N.119, E:N.119 Salt bridges: E:H.59, E:R.92, E:R.109 pi-Stacking: E:F.64 ADP.18: 14 residues within 4Å: Chain D: E.155 Chain F: K.16, Y.56, H.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: PO4.16, MG.17 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.16, F:R.62, F:N.119, F:N.119 Water bridges: F:T.98 Salt bridges: F:H.59, F:R.92, F:R.109 pi-Stacking: F:F.64, F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Admiraal, S.J. et al., Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase. Biochemistry (1999)

Release Date

1999-06-15

Peptides

NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NUCLEOSIDE DIPHOSPHATE KINASE

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