SMTL ID : 7txu.1

Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 Å

Oligo State

hetero-4-8-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: D.431, E.450 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.431, A:E.450 MG.2: 2 residues within 4Å: Chain A: H.586 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.586 MG.3: 4 residues within 4Å: Chain A: T.500, T.522, E.558 Ligands: ATP.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.500, A:T.522, A:E.558, A:E.558 MG.7: 3 residues within 4Å: Chain B: D.431, E.450 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.431, B:E.450 MG.8: 2 residues within 4Å: Chain B: H.586 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.586 MG.9: 4 residues within 4Å: Chain B: T.500, T.522, E.558 Ligands: ATP.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:T.500, B:T.522, B:E.558, B:E.558 MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: D.431, E.450 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.431, C:E.450 MG.15: 2 residues within 4Å: Chain C: H.586 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.586 MG.16: 4 residues within 4Å: Chain C: T.500, T.522, E.558 Ligands: ATP.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.500, C:T.522, C:E.558, C:E.558 MG.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: D.431, E.450 Ligands: ATP.25 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.431, D:E.450 MG.22: 2 residues within 4Å: Chain D: H.586 Ligands: ATP.26 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.586 MG.23: 4 residues within 4Å: Chain D: T.500, T.522, E.558 Ligands: ATP.26 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:T.500, D:T.522, D:E.558, D:E.558 MG.27: 1 residues within 4Å: Chain I: D.4 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain L: D.4 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.59, H.79, H.83 Chain I: D.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.59, A:H.79, A:H.83 ZN.10: 4 residues within 4Å: Chain B: C.59, H.79, H.83 Chain J: D.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.59, B:H.79, B:H.83 ZN.17: 4 residues within 4Å: Chain C: C.59, H.79, H.83 Chain K: D.4 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.59, C:H.79, C:H.83 ZN.24: 4 residues within 4Å: Chain D: C.59, H.79, H.83 Chain L: D.4 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.59, D:H.79, D:H.83

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 15 residues within 4Å: Chain A: V.259, K.261, H.267, G.268, I.271, I.273, E.300, R.301, Y.302, Y.303, D.307, V.433, V.449, E.450 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.261, A:H.267, A:E.300, A:E.300, A:Y.303, A:D.307, A:D.307, A:E.450 Salt bridges: A:K.220, A:K.261 ATP.6: 19 residues within 4Å: Chain A: T.496, N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, R.731, D.745, A.751, G.752, A.755, V.756 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.498, A:K.499, A:T.500, A:T.500, A:T.501, A:N.581, A:N.696, A:D.745 Salt bridges: A:K.499, A:K.499, A:R.731 pi-Stacking: A:F.692 ATP.11: 15 residues within 4Å: Chain B: V.259, K.261, H.267, G.268, I.271, I.273, E.300, R.301, Y.302, Y.303, D.307, V.433, V.449, E.450 Ligands: MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.261, B:H.267, B:E.300, B:Y.303, B:D.307 Salt bridges: B:K.220, B:K.261 ATP.12: 19 residues within 4Å: Chain B: T.496, N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, R.731, D.745, A.751, G.752, A.755, V.756 Ligands: MG.8, MG.9 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.498, B:K.499, B:T.500, B:T.500, B:T.501, B:T.501, B:T.522, B:N.581, B:N.696, B:D.745 Salt bridges: B:K.499, B:K.499, B:R.731 pi-Stacking: B:F.692 ATP.18: 15 residues within 4Å: Chain C: V.259, K.261, H.267, G.268, I.271, I.273, E.300, R.301, Y.302, Y.303, D.307, V.433, V.449, E.450 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.261, C:H.267, C:E.300, C:Y.303, C:D.307 Salt bridges: C:K.220, C:K.261 ATP.19: 19 residues within 4Å: Chain C: T.496, N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, R.731, D.745, A.751, G.752, A.755, V.756 Ligands: MG.15, MG.16 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.498, C:K.499, C:T.500, C:T.500, C:T.501, C:T.501, C:T.522, C:N.581, C:N.696, C:D.745 Salt bridges: C:K.499, C:K.499, C:R.731 pi-Stacking: C:F.692 ATP.25: 15 residues within 4Å: Chain D: V.259, K.261, H.267, G.268, I.271, I.273, E.300, R.301, Y.302, Y.303, D.307, V.433, V.449, E.450 Ligands: MG.21 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.261, D:H.267, D:E.300, D:E.300, D:Y.303, D:D.307, D:D.307, D:E.450 Salt bridges: D:K.220, D:K.261 ATP.26: 19 residues within 4Å: Chain D: T.496, N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, R.731, D.745, A.751, G.752, A.755, V.756 Ligands: MG.22, MG.23 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.498, D:K.499, D:T.500, D:T.500, D:T.501, D:N.581, D:N.696, D:D.745 Salt bridges: D:K.499, D:K.499, D:R.731 pi-Stacking: D:F.692

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharon, I. et al., A cryptic third active site in cyanophycin synthetase creates primers for polymerization. Nat Commun (2022)

Release Date

2022-06-01

Peptides

Cyanophycin synthase: ABCD
16x(Asp-Arg): EFGHIJKL

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

Cyanophycin synthase

16x(Asp-Arg)

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