SMTL ID : 1wkl.2 (1 other biounit)

Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with ATP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-12-mer

Ligands

6 x PHS: PHOSPHONIC ACID(Non-covalent)

PHS.1: 6 residues within 4Å: Chain A: M.7, K.9, H.48, Y.49, H.115 Ligands: ADP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.49, A:Y.49 Salt bridges: A:K.9, A:H.48, A:H.115 PHS.5: 6 residues within 4Å: Chain C: M.7, K.9, H.48, Y.49, H.115 Ligands: ADP.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.49, C:Y.49 Salt bridges: C:K.9, C:H.48, C:H.115 PHS.9: 6 residues within 4Å: Chain E: M.7, K.9, H.48, Y.49, H.115 Ligands: ADP.10 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.49, E:Y.49 Salt bridges: E:K.9, E:H.48, E:H.115 PHS.13: 6 residues within 4Å: Chain G: M.7, K.9, H.48, Y.49, H.115 Ligands: ADP.14 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Y.49 Salt bridges: G:K.9, G:H.48, G:H.115 PHS.17: 6 residues within 4Å: Chain I: M.7, K.9, H.48, Y.49, H.115 Ligands: ADP.18 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Y.49 Salt bridges: I:K.9, I:H.48, I:H.115 PHS.21: 6 residues within 4Å: Chain K: M.7, K.9, H.48, Y.49, H.115 Ligands: ADP.22 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:Y.49 Salt bridges: K:K.9, K:H.48, K:H.115

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

ADP.2: 12 residues within 4Å: Chain A: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112 Ligands: PHS.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.9, A:Y.49, A:T.91, A:T.91, A:I.109, A:N.112, A:N.112 Salt bridges: A:K.9, A:R.85, A:R.102 pi-Stacking: A:F.57, A:F.57 ADP.6: 12 residues within 4Å: Chain C: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112 Ligands: PHS.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.9, C:Y.49, C:T.91, C:T.91, C:I.109, C:N.112, C:N.112 Salt bridges: C:K.9, C:R.85, C:R.102 pi-Stacking: C:F.57, C:F.57 ADP.10: 12 residues within 4Å: Chain E: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112 Ligands: PHS.9 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.9, E:Y.49, E:T.91, E:T.91, E:I.109, E:N.112, E:N.112 Salt bridges: E:K.9, E:R.85, E:R.102 pi-Stacking: E:F.57, E:F.57 ADP.14: 12 residues within 4Å: Chain G: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112 Ligands: PHS.13 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:K.9, G:T.91, G:I.109, G:N.112, G:N.112 Salt bridges: G:K.9, G:R.85, G:R.102 pi-Stacking: G:F.57, G:F.57 ADP.18: 12 residues within 4Å: Chain I: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112 Ligands: PHS.17 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:K.9, I:T.91, I:I.109, I:N.112, I:N.112 Salt bridges: I:K.9, I:R.85, I:R.102 pi-Stacking: I:F.57, I:F.57 ADP.22: 12 residues within 4Å: Chain K: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112 Ligands: PHS.21 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:K.9, K:T.91, K:I.109, K:N.112, K:N.112 Salt bridges: K:K.9, K:R.85, K:R.102 pi-Stacking: K:F.57, K:F.57

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain B: R.85, M.88, R.102, H.115, G.116 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain D: R.85, M.88, R.102, H.115, G.116 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain F: R.85, M.88, R.102, H.115, G.116 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain H: R.85, M.88, R.102, H.115, G.116 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) MG.19: 6 residues within 4Å: Chain J: R.85, M.88, R.102, H.115, G.116 Ligands: ATP.20 No protein-ligand interaction detected (PLIP) MG.23: 6 residues within 4Å: Chain L: R.85, M.88, R.102, H.115, G.116 Ligands: ATP.24 No protein-ligand interaction detected (PLIP)

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 13 residues within 4Å: Chain B: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116 Ligands: MG.3 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain J Hydrogen bonds: B:K.9, B:K.9, B:R.102, B:N.112, B:G.116 Salt bridges: B:K.9, B:H.52, B:R.85, B:H.115, J:K.94, J:K.94 pi-Stacking: B:F.57, B:F.57 Water bridges: J:H.92 ATP.8: 13 residues within 4Å: Chain D: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116 Ligands: MG.7 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain H Hydrogen bonds: D:K.9, D:K.9, D:R.102, D:N.112, D:G.116 Salt bridges: D:K.9, D:H.52, D:R.85, D:H.115, H:K.94, H:K.94 pi-Stacking: D:F.57, D:F.57 Water bridges: H:H.92 ATP.12: 13 residues within 4Å: Chain F: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116 Ligands: MG.11 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain L Hydrogen bonds: F:K.9, F:K.9, F:R.102, F:N.112, F:G.116 Salt bridges: F:K.9, F:H.52, F:R.85, F:H.115, L:K.94, L:K.94 pi-Stacking: F:F.57, F:F.57 Water bridges: L:H.92 ATP.16: 13 residues within 4Å: Chain H: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116 Ligands: MG.15 16 PLIP interactions: 3 interactions with chain D, 13 interactions with chain H Water bridges: D:H.92 Salt bridges: D:K.94, D:K.94, H:K.9, H:H.52, H:R.85, H:H.115 Hydrogen bonds: H:K.9, H:K.9, H:Y.49, H:T.91, H:R.102, H:N.112, H:G.116 pi-Stacking: H:F.57, H:F.57 ATP.20: 13 residues within 4Å: Chain J: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116 Ligands: MG.19 16 PLIP interactions: 13 interactions with chain J, 3 interactions with chain B Hydrogen bonds: J:K.9, J:K.9, J:Y.49, J:T.91, J:R.102, J:N.112, J:G.116 Salt bridges: J:K.9, J:H.52, J:R.85, J:H.115, B:K.94, B:K.94 pi-Stacking: J:F.57, J:F.57 Water bridges: B:H.92 ATP.24: 13 residues within 4Å: Chain L: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116 Ligands: MG.23 16 PLIP interactions: 13 interactions with chain L, 3 interactions with chain F Hydrogen bonds: L:K.9, L:K.9, L:Y.49, L:T.91, L:R.102, L:N.112, L:G.116 Salt bridges: L:K.9, L:H.52, L:R.85, L:H.115, F:K.94, F:K.94 pi-Stacking: L:F.57, L:F.57 Water bridges: F:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeishi, S. et al., Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8. To be Published

Release Date

2005-08-23

Peptides

nucleotide diphosphate kinase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

nucleotide diphosphate kinase

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