SMTL ID : 8io8.1

Cryo-EM structure of cyanobacteria phosphoketolase complexed with AMPPNPin dimeric assembly

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 14 residues within 4Å: Chain A: P.702, W.703, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain B: K.707, Y.710, R.711, H.715 Ligands: ANP.4 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.710, B:R.711, A:L.718, A:V.720, A:R.753 pi-Stacking: B:Y.710, B:Y.710, A:H.706 Salt bridges: A:H.706 ANP.4: 13 residues within 4Å: Chain A: H.706, K.707, Y.710, R.711 Chain B: P.702, W.703, H.706, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.1 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:L.718, B:H.719, B:V.720, B:R.721, B:R.721, B:R.753, A:Y.710, A:Y.710, A:R.711, A:R.711 Salt bridges: B:H.706 pi-Stacking: B:H.706, B:H.706, A:Y.710, A:Y.710

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 21 residues within 4Å: Chain A: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Chain B: L.468, E.470, F.495 Ligands: MG.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.215, A:I.215, B:L.468 Hydrogen bonds: A:S.63, A:G.151, A:L.153, A:G.177, A:G.179, A:E.180, A:H.209, A:N.211, A:K.214, A:H.313 Salt bridges: A:H.93, A:H.93, A:K.293, A:K.293 pi-Stacking: B:F.495 TPP.5: 21 residues within 4Å: Chain A: L.468, E.470, F.495 Chain B: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Ligands: MG.6 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.215, B:I.215, A:L.468 Hydrogen bonds: B:G.151, B:L.153, B:D.178, B:G.179, B:E.180, B:H.209, B:N.211 Salt bridges: B:H.93, B:H.93, B:H.209, B:K.293, B:K.293 pi-Stacking: A:F.495

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.178, N.211, Y.213 Ligands: TPP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.178, A:Y.213 MG.6: 5 residues within 4Å: Chain B: D.178, N.211, Y.213, K.214 Ligands: TPP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.178, B:Y.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, K.J. et al., An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria. Nat Metab (2023)

Release Date

2023-06-28

Peptides

Probable phosphoketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable phosphoketolase

Related Entries With Identical Sequence