SMTL ID : 3afo.1

Crystal Structure of Yeast NADH Kinase complexed with NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 22 residues within 4Å: Chain A: D.124, G.125, L.128, H.129, G.151, F.152, L.153, N.200, D.201, T.238, T.241, A.242, Y.243, S.246, D.304, G.305 Chain D: R.206, P.210, L.212, D.230, C.265, R.267 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:D.124, A:G.125, A:N.200, A:N.200, A:D.201, A:Y.243, A:S.246, A:S.246, A:D.304, D:D.230, D:R.267 Water bridges: A:D.124, A:D.124, A:S.244, D:L.212, D:R.267, D:R.267, D:R.267 pi-Stacking: A:Y.243 Hydrophobic interactions: D:L.212 NAI.4: 21 residues within 4Å: Chain B: D.124, G.125, L.128, H.129, G.151, F.152, L.153, N.200, D.201, T.238, T.241, A.242, Y.243, S.246, D.304, G.305 Chain C: R.206, L.212, D.230, C.265, R.267 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.125, B:N.200, B:D.201, B:T.238, B:T.241, B:Y.243, B:S.246, B:S.246, B:D.304, C:D.230, C:R.267 Water bridges: B:D.124, B:D.124, B:D.124, B:L.150, C:H.211, C:H.211, C:R.267 pi-Stacking: B:Y.243 Hydrophobic interactions: C:L.212 NAI.7: 22 residues within 4Å: Chain B: R.206, P.210, L.212, D.230, C.265, R.267 Chain C: D.124, G.125, L.128, H.129, G.151, F.152, L.153, N.200, D.201, T.238, T.241, A.242, Y.243, S.246, D.304, G.305 20 PLIP interactions: 7 interactions with chain B, 13 interactions with chain C Hydrophobic interactions: B:L.212 Hydrogen bonds: B:D.230, B:R.267, C:D.124, C:G.125, C:N.200, C:N.200, C:D.201, C:Y.243, C:S.246, C:S.246, C:D.304 Water bridges: B:L.212, B:R.267, B:R.267, B:R.267, C:D.124, C:D.124, C:S.244 pi-Stacking: C:Y.243 NAI.10: 21 residues within 4Å: Chain A: R.206, L.212, D.230, C.265, R.267 Chain D: D.124, G.125, L.128, H.129, G.151, F.152, L.153, N.200, D.201, T.238, T.241, A.242, Y.243, S.246, D.304, G.305 20 PLIP interactions: 14 interactions with chain D, 6 interactions with chain A Hydrogen bonds: D:G.125, D:N.200, D:D.201, D:T.238, D:T.241, D:Y.243, D:S.246, D:S.246, D:D.304, A:D.230, A:R.267 Water bridges: D:D.124, D:D.124, D:D.124, D:L.150, A:H.211, A:H.211, A:R.267 pi-Stacking: D:Y.243 Hydrophobic interactions: A:L.212

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 9 residues within 4Å: Chain A: F.152, L.153, P.155, L.176, R.178, P.254, D.363, W.364, G.367 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.155, A:L.176, A:P.254, A:D.363, A:W.364 Hydrogen bonds: A:F.152, A:R.178, A:R.178 MPD.3: 5 residues within 4Å: Chain A: R.172, A.173, K.174, A.358, K.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 MPD.5: 4 residues within 4Å: Chain B: A.173, K.174, A.358, K.359 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.173 Hydrogen bonds: B:K.174 MPD.6: 9 residues within 4Å: Chain B: F.152, L.153, P.155, L.176, R.178, P.254, D.363, W.364, G.367 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.152, B:P.155, B:L.176, B:P.254, B:W.364 Hydrogen bonds: B:F.152, B:R.178, B:R.178 MPD.8: 9 residues within 4Å: Chain C: F.152, L.153, P.155, L.176, R.178, P.254, D.363, W.364, G.367 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.155, C:L.176, C:P.254, C:D.363, C:W.364 Hydrogen bonds: C:F.152, C:R.178, C:R.178 MPD.9: 5 residues within 4Å: Chain C: R.172, A.173, K.174, A.358, K.359 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.174 MPD.11: 4 residues within 4Å: Chain D: A.173, K.174, A.358, K.359 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.173 Hydrogen bonds: D:K.174 MPD.12: 9 residues within 4Å: Chain D: F.152, L.153, P.155, L.176, R.178, P.254, D.363, W.364, G.367 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.152, D:P.155, D:L.176, D:P.254, D:W.364 Hydrogen bonds: D:F.152, D:R.178, D:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ando, T. et al., The structural factor conferring NADH kinase activity on yeast mitochondrial Pos5. To be Published

Release Date

2011-03-16

Peptides

NADH kinase POS5: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NADH kinase POS5