SMTL ID : 7txv.1

Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

hetero-4-8-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.450, N.452 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.450 MG.2: 4 residues within 4Å: Chain A: D.431, E.450, N.452 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.431 MG.3: 3 residues within 4Å: Chain A: T.496, H.586 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: T.500, T.522, E.558 Ligands: ATP.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.500, A:T.522, A:E.558, A:E.558 MG.8: 3 residues within 4Å: Chain B: E.450, N.452 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.450 MG.9: 4 residues within 4Å: Chain B: D.431, E.450, N.452 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.431 MG.10: 3 residues within 4Å: Chain B: T.496, H.586 Ligands: ATP.14 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: T.500, T.522, E.558 Ligands: ATP.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:T.500, B:T.522, B:E.558, B:E.558 MG.15: 3 residues within 4Å: Chain C: E.450, N.452 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.450 MG.16: 4 residues within 4Å: Chain C: D.431, E.450, N.452 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.431 MG.17: 3 residues within 4Å: Chain C: T.496, H.586 Ligands: ATP.21 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: T.500, T.522, E.558 Ligands: ATP.21 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.500, C:T.522, C:E.558, C:E.558 MG.22: 3 residues within 4Å: Chain D: E.450, N.452 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.450 MG.23: 4 residues within 4Å: Chain D: D.431, E.450, N.452 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.431 MG.24: 3 residues within 4Å: Chain D: T.496, H.586 Ligands: ATP.28 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain D: T.500, T.522, E.558 Ligands: ATP.28 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:T.500, D:T.522, D:E.558, D:E.558

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: C.59, F.67, H.79, H.83 Chain I: D.4, D.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.59, A:H.79, A:H.83 ZN.12: 6 residues within 4Å: Chain B: C.59, F.67, H.79, H.83 Chain J: D.4, D.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.59, B:H.79, B:H.83 ZN.19: 6 residues within 4Å: Chain C: C.59, F.67, H.79, H.83 Chain K: D.4, D.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.59, C:H.79, C:H.83 ZN.26: 6 residues within 4Å: Chain D: C.59, F.67, H.79, H.83 Chain L: D.4, D.6 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.6: 16 residues within 4Å: Chain A: P.235, 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 Ligands: MG.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.261, A:H.267, A:E.300, A:E.300, A:Y.303, A:D.307 Salt bridges: A:K.261 ATP.7: 13 residues within 4Å: Chain A: N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, A.755 Ligands: MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.498, A:K.499, A:T.500, A:T.500, A:T.501, A:T.501, A:T.522, A:N.581, A:N.696 Salt bridges: A:K.499, A:K.499 pi-Stacking: A:F.692, A:F.692 ATP.13: 16 residues within 4Å: Chain B: P.235, 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 Ligands: MG.8, MG.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.261, B:H.267, B:E.300, B:E.300, B:Y.303, B:D.307 Salt bridges: B:K.261 ATP.14: 13 residues within 4Å: Chain B: N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, A.755 Ligands: MG.10, MG.11 13 PLIP interactions: 13 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 Salt bridges: B:K.499, B:K.499 pi-Stacking: B:F.692, B:F.692 ATP.20: 16 residues within 4Å: Chain C: P.235, 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 Ligands: MG.15, MG.16 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, C:D.307 Salt bridges: C:K.261 ATP.21: 13 residues within 4Å: Chain C: N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, A.755 Ligands: MG.17, MG.18 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.498, C:K.499, C:T.500, C:T.500, C:T.501, C:T.522, C:T.522, C:N.581, C:N.696 Salt bridges: C:K.499, C:K.499 pi-Stacking: C:F.692, C:F.692 ATP.27: 16 residues within 4Å: Chain D: P.235, 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 Ligands: MG.22, MG.23 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.261, D:H.267, D:E.300, D:Y.303, D:D.307, D:D.307 Salt bridges: D:K.261 ATP.28: 13 residues within 4Å: Chain D: N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, N.696, A.755 Ligands: MG.24, MG.25 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.498, D:K.499, D:T.500, D:T.500, D:T.501, D:T.522, D:T.522, D:N.581, D:N.696 Salt bridges: D:K.499, D:K.499 pi-Stacking: D:F.692, 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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