SMTL ID : 8io9.1

Cryo-EM structure of cyanobacteria phosphoketolase complexed with AMPPNP in dodecameric assembly

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

ANP.1: 12 residues within 4Å: Chain A: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain B: H.706, Y.710, R.711 Ligands: ANP.4 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.718, A:H.719, A:V.720, A:R.721, A:R.721, A:R.753, A:R.753, B:Y.710, B:R.711 Salt bridges: A:H.706 pi-Stacking: A:H.706, B:Y.710 ANP.4: 14 residues within 4Å: Chain A: H.706, K.707, Y.710, R.711 Chain B: P.702, W.703, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.1 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.711, B:V.720, B:R.721, B:R.721, B:R.753, B:R.753 pi-Stacking: A:Y.710, B:H.706 Salt bridges: B:H.706 ANP.7: 12 residues within 4Å: Chain C: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain D: H.706, Y.710, R.711 Ligands: ANP.10 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:L.718, C:H.719, C:V.720, C:R.721, C:R.721, C:R.753, C:R.753, D:Y.710, D:Y.710, D:R.711 Salt bridges: C:H.706 pi-Stacking: C:H.706, D:Y.710 ANP.10: 14 residues within 4Å: Chain C: H.706, K.707, Y.710, R.711 Chain D: P.702, W.703, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.7 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:R.711, C:R.711, D:W.703, D:V.720, D:R.721, D:R.721, D:R.753, D:R.753 pi-Stacking: C:Y.710, D:H.706 Salt bridges: D:H.706 ANP.13: 12 residues within 4Å: Chain E: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain F: H.706, Y.710, R.711 Ligands: ANP.16 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:L.718, E:H.719, E:V.720, E:R.721, E:R.721, E:R.753, E:R.753, F:Y.710 Salt bridges: E:H.706 pi-Stacking: E:H.706, F:Y.710 ANP.16: 12 residues within 4Å: Chain E: H.706, Y.710, R.711 Chain F: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.13 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:L.718, F:V.720, F:R.721, F:R.721, F:R.753, F:R.753, E:Y.710, E:R.711 Salt bridges: F:H.706 pi-Stacking: F:H.706, E:Y.710 ANP.19: 12 residues within 4Å: Chain G: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain H: H.706, Y.710, R.711 Ligands: ANP.22 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:L.718, G:H.719, G:V.720, G:R.721, G:R.721, G:R.753, G:R.753, H:Y.710 Salt bridges: G:H.706 pi-Stacking: G:H.706, H:Y.710 ANP.22: 12 residues within 4Å: Chain G: H.706, Y.710, R.711 Chain H: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.19 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:L.718, H:V.720, H:R.721, H:R.721, H:R.753, H:R.753, G:Y.710 Salt bridges: H:H.706 pi-Stacking: H:H.706, G:Y.710 ANP.25: 12 residues within 4Å: Chain I: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain J: H.706, Y.710, R.711 Ligands: ANP.28 13 PLIP interactions: 9 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:L.718, I:H.719, I:V.720, I:R.721, I:R.721, I:R.753, I:R.753, J:Y.710, J:Y.710, J:R.711 Salt bridges: I:H.706 pi-Stacking: I:H.706, J:Y.710 ANP.28: 12 residues within 4Å: Chain I: H.706, Y.710, R.711 Chain J: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.25 9 PLIP interactions: 1 interactions with chain I, 8 interactions with chain J pi-Stacking: I:Y.710, J:H.706 Hydrogen bonds: J:L.718, J:V.720, J:R.721, J:R.721, J:R.753, J:R.753 Salt bridges: J:H.706 ANP.31: 12 residues within 4Å: Chain K: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Chain L: H.706, Y.710, R.711 Ligands: ANP.34 11 PLIP interactions: 8 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:H.719, K:V.720, K:R.721, K:R.721, K:R.753, K:R.753, L:Y.710, L:R.711 Salt bridges: K:H.706 pi-Stacking: K:H.706, L:Y.710 ANP.34: 12 residues within 4Å: Chain K: H.706, Y.710, R.711 Chain L: P.702, H.706, H.715, L.718, H.719, V.720, R.721, R.753 Ligands: ANP.31 10 PLIP interactions: 8 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:L.718, L:V.720, L:R.721, L:R.721, L:R.753, L:R.753, K:Y.710 Salt bridges: L:H.706 pi-Stacking: L:H.706, K:Y.710

12 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 21 residues within 4Å: Chain A: S.63, P.91, H.93, G.151, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Chain B: E.427, L.468, F.495 Ligands: MG.3 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.183, A:I.215, B:L.468 Hydrogen bonds: A:G.151, A:L.153, A:G.179, A:E.180, A:N.211, A:N.211 Salt bridges: A:H.93, A:K.293, A:K.293 pi-Stacking: B:F.495 TPP.5: 20 residues within 4Å: Chain A: L.468, F.495 Chain B: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, I.215, K.293, H.313 Ligands: MG.6 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.183, B:I.215, A:L.468 Hydrogen bonds: B:G.151, B:L.153, B:G.177, B:D.178, B:G.179, B:E.180, B:H.209, B:H.313 Salt bridges: B:H.93, B:K.293, B:K.293 pi-Stacking: A:F.495 TPP.8: 21 residues within 4Å: Chain C: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, I.215, K.293, H.313 Chain D: E.427, L.468, F.495 Ligands: MG.9 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:T.183, C:I.215, D:L.468 Hydrogen bonds: C:G.151, C:L.153, C:G.179, C:E.180, C:N.211, C:N.211 Salt bridges: C:H.93, C:K.293, C:K.293 pi-Stacking: D:F.495 TPP.11: 19 residues within 4Å: Chain C: L.468, F.495 Chain D: S.63, P.91, H.93, G.151, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, I.215, K.293, H.313 Ligands: MG.12 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:T.183, D:I.215, C:L.468 Hydrogen bonds: D:G.151, D:L.153, D:G.177, D:D.178, D:G.179, D:E.180, D:N.211, D:H.313 Salt bridges: D:H.93, D:K.293, D:K.293 pi-Stacking: C:F.495 TPP.14: 21 residues within 4Å: Chain E: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, I.215, K.293, H.313 Chain F: E.427, L.468, F.495 Ligands: MG.15 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:T.183, E:I.215, F:L.468 Hydrogen bonds: E:G.151, E:L.153, E:G.179, E:E.180, E:N.211, E:N.211 Salt bridges: E:H.93, E:K.293, E:K.293 pi-Stacking: F:F.495 TPP.17: 20 residues within 4Å: Chain E: L.468, F.495 Chain F: S.63, P.91, H.93, G.151, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Ligands: MG.18 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:T.183, F:I.215, E:L.468 Hydrogen bonds: F:G.151, F:L.153, F:G.177, F:D.178, F:G.179, F:E.180, F:N.211, F:H.313 Salt bridges: F:H.93, F:K.293, F:K.293 pi-Stacking: E:F.495 TPP.20: 21 residues within 4Å: Chain G: S.63, P.91, H.93, G.151, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Chain H: E.427, L.468, F.495 Ligands: MG.21 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:T.183, G:I.215, H:L.468 Hydrogen bonds: G:G.151, G:L.153, G:G.179, G:E.180, G:N.211, G:N.211 Salt bridges: G:H.93, G:K.293, G:K.293 pi-Stacking: H:F.495 TPP.23: 20 residues within 4Å: Chain G: L.468, F.495 Chain H: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, I.215, K.293, H.313 Ligands: MG.24 15 PLIP interactions: 13 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:T.183, H:I.215, G:L.468 Hydrogen bonds: H:G.151, H:L.153, H:G.177, H:D.178, H:G.179, H:E.180, H:H.209, H:H.313 Salt bridges: H:H.93, H:K.293, H:K.293 pi-Stacking: G:F.495 TPP.26: 22 residues within 4Å: Chain I: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Chain J: E.427, L.468, F.495 Ligands: MG.27 13 PLIP interactions: 11 interactions with chain I, 2 interactions with chain J Hydrophobic interactions: I:T.183, I:I.215, J:L.468 Hydrogen bonds: I:G.151, I:L.153, I:G.179, I:E.180, I:N.211, I:N.211 Salt bridges: I:H.93, I:K.293, I:K.293 pi-Stacking: J:F.495 TPP.29: 20 residues within 4Å: Chain I: L.468, F.495 Chain J: S.63, P.91, H.93, G.151, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Ligands: MG.30 15 PLIP interactions: 13 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:T.183, J:I.215, I:L.468 Hydrogen bonds: J:G.151, J:L.153, J:G.177, J:D.178, J:G.179, J:E.180, J:N.211, J:H.313 Salt bridges: J:H.93, J:K.293, J:K.293 pi-Stacking: I:F.495 TPP.32: 21 residues within 4Å: Chain K: S.63, P.91, H.93, G.151, E.152, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, I.215, K.293, H.313 Chain L: E.427, L.468, F.495 Ligands: MG.33 13 PLIP interactions: 2 interactions with chain L, 11 interactions with chain K Hydrophobic interactions: L:L.468, K:T.183, K:I.215 pi-Stacking: L:F.495 Hydrogen bonds: K:G.151, K:L.153, K:G.179, K:E.180, K:N.211, K:N.211 Salt bridges: K:H.93, K:K.293, K:K.293 TPP.35: 21 residues within 4Å: Chain K: E.427, L.468, F.495 Chain L: S.63, P.91, H.93, G.151, L.153, G.177, D.178, G.179, E.180, T.183, H.209, N.211, Y.213, K.214, I.215, K.293, H.313 Ligands: MG.36 15 PLIP interactions: 13 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:T.183, L:I.215, K:L.468 Hydrogen bonds: L:G.151, L:L.153, L:G.177, L:D.178, L:G.179, L:E.180, L:N.211, L:H.313 Salt bridges: L:H.93, L:K.293, L:K.293 pi-Stacking: K:F.495

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.178, N.211, Y.213, K.293 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.293 Ligands: TPP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.178, B:Y.213 MG.9: 5 residues within 4Å: Chain C: D.178, N.211, Y.213, K.293 Ligands: TPP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.178, C:Y.213 MG.12: 5 residues within 4Å: Chain D: D.178, N.211, Y.213, K.293 Ligands: TPP.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.178, D:Y.213 MG.15: 5 residues within 4Å: Chain E: D.178, N.211, Y.213, K.293 Ligands: TPP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.178, E:Y.213 MG.18: 5 residues within 4Å: Chain F: D.178, N.211, Y.213, K.293 Ligands: TPP.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.178, F:Y.213 MG.21: 5 residues within 4Å: Chain G: D.178, N.211, Y.213, K.293 Ligands: TPP.20 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.178, G:Y.213 MG.24: 5 residues within 4Å: Chain H: D.178, N.211, Y.213, K.293 Ligands: TPP.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.178, H:Y.213 MG.27: 5 residues within 4Å: Chain I: D.178, N.211, Y.213, K.293 Ligands: TPP.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.178, I:Y.213 MG.30: 5 residues within 4Å: Chain J: D.178, N.211, Y.213, K.293 Ligands: TPP.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.178, J:Y.213 MG.33: 5 residues within 4Å: Chain K: D.178, N.211, Y.213, K.293 Ligands: TPP.32 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.178, K:Y.213 MG.36: 5 residues within 4Å: Chain L: D.178, N.211, Y.213, K.293 Ligands: TPP.35 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.178, L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Probable phosphoketolase

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