SMTL ID : 9fl7.1

Cryo-EM structure of human AK2 bound to reduced human AIFM1 (residues 102-613), class 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 17 residues within 4Å: Chain A: L.172, G.213, G.214, F.215, L.216, P.240, E.241, K.247, I.273, V.303, E.358, H.359, W.388, S.389 Chain C: A.14, P.16 Ligands: FAD.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.215, A:L.216 Hydrogen bonds: A:G.213, A:G.213, A:F.215, A:L.216, A:E.241, A:E.241, A:G.304, A:W.388, C:A.14 Salt bridges: A:K.247 NAD.3: 15 residues within 4Å: Chain B: L.172, G.213, G.214, F.215, L.216, E.219, A.302, V.303, G.304, L.305, E.358, H.359, W.388, S.389 Ligands: FAD.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.215, B:F.215 Hydrogen bonds: B:G.213, B:G.213, B:G.214, B:F.215, B:L.216, B:E.358, B:W.388

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 25 residues within 4Å: Chain A: G.43, G.44, G.45, T.46, A.47, E.69, R.77, P.78, S.81, K.137, V.138, A.164, T.165, G.166, F.189, R.190, K.191, L.216, N.308, E.310, D.343, E.358, H.359, H.360 Ligands: NAD.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.189, A:L.216 Hydrogen bonds: A:G.44, A:T.46, A:A.47, A:E.69, A:E.69, A:R.77, A:S.81, A:V.138, A:V.138, A:K.191, A:K.191, A:N.308, A:E.310, A:D.343, A:H.360 Salt bridges: A:R.77, A:R.190 FAD.4: 27 residues within 4Å: Chain B: G.43, G.44, G.45, T.46, A.47, S.68, E.69, D.70, R.77, P.78, L.80, S.81, K.136, K.137, V.138, A.164, T.165, G.166, R.190, E.310, D.343, H.359, H.360, A.363, F.387, W.388 Ligands: NAD.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.77, B:L.80 Hydrogen bonds: B:G.44, B:G.44, B:T.46, B:T.46, B:A.47, B:E.69, B:D.70, B:V.138, B:V.138, B:R.190, B:D.343, B:H.359, B:H.360 Salt bridges: B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schildhauer, F. et al., An NADH-controlled gatekeeper of ATP synthase. Mol.Cell (2025)

Release Date

2025-05-14

Peptides

Apoptosis-inducing factor 1, mitochondrial: AB
Adenylate kinase 2, mitochondrial: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Apoptosis-inducing factor 1, mitochondrial

Adenylate kinase 2, mitochondrial