SMTL ID : 7r4m.1

Crystal structure of mitochondrial NAD kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 25 residues within 4Å: Chain A: G.109, D.110, G.111, L.114, S.137, E.138, G.139, H.140, L.141, N.225, E.226, T.263, K.266, A.267, W.268, N.271, D.361, G.362 Chain B: S.235, A.237, S.255, E.328, I.330, N.332 Ligands: CA.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.110, A:G.111, A:E.138, A:G.139, A:N.225, A:E.226, A:T.263, A:W.268, A:N.271, A:D.361, B:E.328, B:E.328, B:N.332 Water bridges: A:T.112, A:T.112 pi-Stacking: A:W.268, A:W.268 Hydrophobic interactions: B:I.330 NAP.3: 25 residues within 4Å: Chain A: S.235, A.237, S.255, E.328, I.330, N.332 Chain B: G.109, D.110, G.111, L.114, S.137, E.138, G.139, H.140, L.141, N.225, E.226, T.263, K.266, A.267, W.268, N.271, D.361, G.362 Ligands: CA.4 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.110, B:D.110, B:G.111, B:E.138, B:G.139, B:N.225, B:E.226, B:T.263, B:W.268, B:N.271, B:D.361, A:E.328, A:N.332 Water bridges: B:T.112, B:T.112 pi-Stacking: B:W.268, B:W.268 Hydrophobic interactions: A:I.330

2 x CA: CALCIUM ION(Non-functional Binders)

CA.2: 1 residues within 4Å: Ligands: NAP.1 No protein-ligand interaction detected (PLIP) CA.4: 1 residues within 4Å: Ligands: NAP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mary, C. et al., Crystal structure of human NADK2 reveals a dimeric organization and active site occlusion by lysine acetylation. Mol.Cell (2022)

Release Date

2022-07-06

Peptides

NAD kinase 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NAD kinase 2, mitochondrial

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