SMTL ID : 7wae.1

Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS, 4x(beta-Asp-Arg), and aspartate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ASP- ASP- ASP- ASP: 4x(beta-Asp-Arg)(Non-covalent)

ASP-ASP-ASP-ASP.1: 8 residues within 4Å: Chain B: S.166, R.309, A.453, A.454, P.455, G.456 Ligands: ARG.25, ARG.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.166, B:A.454, B:A.454, B:G.456 Salt bridges: B:R.309 ASP-ASP-ASP-ASP.2: 11 residues within 4Å: Chain D: S.166, N.266, R.309, N.452, A.453, A.454, P.455, G.456 Ligands: ASP.24, ARG.27, ARG.28 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:N.452 Hydrogen bonds: D:S.166, D:N.266, D:A.454, D:A.454, D:G.456 Salt bridges: D:R.309 ASP-ASP-ASP-ASP.3: 11 residues within 4Å: Chain A: S.166, A.203, T.204, N.266, R.309, A.453, A.454, P.455, G.456 Ligands: ARG.29, ARG.30 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.166, A:N.266, A:A.454, A:A.454, A:A.454, A:G.456 Salt bridges: A:R.309 ASP-ASP-ASP-ASP.4: 12 residues within 4Å: Chain C: S.166, A.203, N.266, H.267, R.309, N.452, A.453, A.454, P.455, G.456 Ligands: ARG.31, ARG.32 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.452 Hydrogen bonds: C:S.166, C:T.204, C:N.266, C:H.267, C:A.454, C:A.454, C:G.456 Salt bridges: C:R.309

11 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: E.450, N.452 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.450, A:E.450 MG.6: 5 residues within 4Å: Chain A: T.500, T.522, E.558, R.731 Ligands: AGS.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.500, A:T.522, A:E.558 MG.9: 4 residues within 4Å: Chain B: E.450, N.452 Ligands: MG.10, AGS.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.450, B:E.450 MG.10: 4 residues within 4Å: Chain B: D.431, E.450 Ligands: MG.9, AGS.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.431, B:E.450 MG.11: 5 residues within 4Å: Chain B: T.500, T.522, E.558, R.731 Ligands: AGS.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.500, B:T.522, B:E.558 MG.14: 4 residues within 4Å: Chain C: N.266, E.450, N.452 Ligands: AGS.17 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.450, C:E.450 MG.15: 5 residues within 4Å: Chain C: R.309, R.323, D.431, E.450 Ligands: AGS.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.450 MG.16: 4 residues within 4Å: Chain C: T.500, T.522, E.558 Ligands: AGS.18 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.500, C:T.522 MG.19: 4 residues within 4Å: Chain D: N.266, E.450, N.452 Ligands: AGS.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.450, D:E.450 MG.20: 4 residues within 4Å: Chain D: R.323, D.431, E.450 Ligands: AGS.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.431, D:E.450 MG.21: 4 residues within 4Å: Chain D: T.500, T.522, E.558 Ligands: AGS.23 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.500, D:T.522

8 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.7: 16 residues within 4Å: Chain A: K.220, 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.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.261, A:H.267, A:G.268, A:E.300, A:Y.303, A:D.307 Salt bridges: A:K.220, A:K.220, A:K.261, A:K.261 AGS.8: 18 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, R.731, M.732, D.745, Y.746, H.748, S.752, A.755 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.499, A:K.499, A:T.500, A:T.501, A:T.501, A:T.501, A:N.581, A:N.696, A:N.696, A:D.745, A:Y.746 Salt bridges: A:K.499, A:R.731 AGS.12: 17 residues within 4Å: Chain B: K.220, P.235, V.259, K.261, H.267, G.268, I.271, I.273, E.300, R.301, Y.303, D.307, V.433, V.449, E.450 Ligands: MG.9, MG.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.261, B:H.267, B:G.268, B:E.300, B:Y.303, B:D.307 Salt bridges: B:K.220, B:K.220, B:K.261, B:K.261 AGS.13: 18 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, R.731, M.732, D.745, Y.746, H.748, S.752, A.755 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.499, B:K.499, B:T.500, B:T.500, B:T.501, B:T.501, B:N.581, B:N.696, B:N.696, B:D.745, B:Y.746 Salt bridges: B:K.499, B:R.731 AGS.17: 21 residues within 4Å: Chain C: K.220, P.235, V.259, K.261, G.265, N.266, H.267, G.268, I.271, I.273, E.300, R.301, Y.302, Y.303, D.307, N.394, V.433, V.449, E.450 Ligands: MG.14, MG.15 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.261, C:N.266, C:H.267, C:H.267, C:G.268, C:E.300, C:E.300, C:Y.303, C:D.307 Salt bridges: C:K.220, C:K.220, C:K.261 AGS.18: 12 residues within 4Å: Chain C: N.497, G.498, K.499, T.500, T.501, T.522, E.558, N.581, F.692, M.693, N.696 Ligands: MG.16 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.499, C:K.499, C:T.500, C:T.501, C:N.581, C:N.696, C:N.696 Salt bridges: C:K.499 pi-Stacking: C:F.692 AGS.22: 21 residues within 4Å: Chain D: K.220, V.259, K.261, G.265, N.266, H.267, G.268, I.271, I.273, E.300, R.301, Y.302, Y.303, D.307, N.394, D.431, V.433, V.449, E.450 Ligands: MG.19, MG.20 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.261, D:N.266, D:H.267, D:H.267, D:G.268, D:E.300, D:E.300, D:Y.303, D:D.307, D:R.323 Salt bridges: D:K.220, D:K.220, D:K.261 AGS.23: 11 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 Ligands: MG.21 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.499, D:K.499, D:T.500, D:T.501, D:N.581, D:N.696, D:N.696 Salt bridges: D:K.499 pi-Stacking: D:F.692

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.24: 7 residues within 4Å: Chain D: R.323, N.394, L.395, S.396, R.458 Ligands: ASP-ASP-ASP-ASP.2, ASP-ASP-ASP-ASP.2 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:N.394, D:R.458, D.24 Salt bridges: D:H.267, D:R.323, D:R.458

8 x ARG: ARGININE(Non-covalent)

ARG.25: 9 residues within 4Å: Chain B: G.164, P.165, S.166, T.167, F.188, A.203, H.353 Ligands: ASP-ASP-ASP-ASP.1, ASP-ASP-ASP-ASP.1 7 PLIP interactions: 7 interactions with chain B, Hydrogen bonds: B:G.164, B:S.166, B:T.167, B:T.167, B:T.167 Salt bridges: B:H.353 pi-Cation interactions: B:F.188 ARG.26: 7 residues within 4Å: Chain B: V.214, A.453, A.454 Chain D: E.215 Ligands: ASP-ASP-ASP-ASP.1, ASP-ASP-ASP-ASP.1, ASP-ASP-ASP-ASP.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, Hydrogen bonds: B:A.453 Salt bridges: D:E.215 ARG.27: 7 residues within 4Å: Chain D: G.164, P.165, S.166, T.167, H.353 Ligands: ASP-ASP-ASP-ASP.2, ASP-ASP-ASP-ASP.2 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:S.166, D:T.167, R.27, R.27 Salt bridges: D:H.353 pi-Cation interactions: D:F.188 ARG.28: 6 residues within 4Å: Chain B: E.215 Chain D: Q.202, N.266, A.453 Ligands: ASP-ASP-ASP-ASP.2, ASP-ASP-ASP-ASP.2 6 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D, 2 Ligand-Ligand interactions Salt bridges: B:E.215 Hydrogen bonds: D:Q.202, D:N.266, D:A.453, R.28, R.28 ARG.29: 8 residues within 4Å: Chain A: G.164, P.165, S.166, T.167, F.188, A.203 Ligands: ASP-ASP-ASP-ASP.3, ASP-ASP-ASP-ASP.3 5 PLIP interactions: 5 interactions with chain A, Hydrogen bonds: A:S.166, A:T.167, A:T.167, A:T.167 pi-Cation interactions: A:F.188 ARG.30: 6 residues within 4Å: Chain A: Q.202, V.214, A.453 Chain C: E.215 Ligands: ASP-ASP-ASP-ASP.3, ASP-ASP-ASP-ASP.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.202, A:A.453 Salt bridges: C:E.215 ARG.31: 8 residues within 4Å: Chain C: G.164, P.165, T.167, F.188, A.203, H.353 Ligands: ASP-ASP-ASP-ASP.4, ASP-ASP-ASP-ASP.4 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:G.164, C:H.353, R.31 pi-Cation interactions: C:F.188 ARG.32: 10 residues within 4Å: Chain A: E.215 Chain C: Q.202, L.205, V.214, C.218, N.266, A.453 Ligands: ASP-ASP-ASP-ASP.4, ASP-ASP-ASP-ASP.4, ASP-ASP-ASP-ASP.4 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: C:Q.202, C:N.266, C:A.454, R.32, R.32 Salt bridges: A:E.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyakawa, T. et al., Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Nat Commun (2022)

Release Date

2022-09-07

Peptides

Cyanophycin synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cyanophycin synthase

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