SMTL ID : 5gqm.1

Crystal structure of in cellulo Wild Type Cypovirus Polyhedra

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-12-mer

Ligands

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: S.30, L.31 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: S.30, L.31 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: S.30, L.31 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain D: S.30, L.31 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain E: S.30, L.31 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain F: S.30, L.31 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain G: S.30, L.31 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain H: S.30, L.31 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain I: S.30, L.31 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain J: S.30, L.31 Ligand excluded by PLIP CL.61: 2 residues within 4Å: Chain K: S.30, L.31 Ligand excluded by PLIP CL.67: 2 residues within 4Å: Chain L: S.30, L.31 Ligand excluded by PLIP

24 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: CTP.6 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: CTP.12 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: CTP.18 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: CTP.24 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Ligands: ATP.23 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Ligands: CTP.30 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Ligands: ATP.29 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Ligands: CTP.36 No protein-ligand interaction detected (PLIP) MG.33: 1 residues within 4Å: Ligands: ATP.35 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Ligands: CTP.42 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Ligands: ATP.41 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Ligands: CTP.48 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Ligands: ATP.47 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Ligands: CTP.54 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Ligands: ATP.53 No protein-ligand interaction detected (PLIP) MG.56: 1 residues within 4Å: Ligands: CTP.60 No protein-ligand interaction detected (PLIP) MG.57: 1 residues within 4Å: Ligands: ATP.59 No protein-ligand interaction detected (PLIP) MG.62: 1 residues within 4Å: Ligands: CTP.66 No protein-ligand interaction detected (PLIP) MG.63: 1 residues within 4Å: Ligands: ATP.65 No protein-ligand interaction detected (PLIP) MG.68: 1 residues within 4Å: Ligands: CTP.72 No protein-ligand interaction detected (PLIP) MG.69: 1 residues within 4Å: Ligands: ATP.71 No protein-ligand interaction detected (PLIP)

12 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 2 residues within 4Å: Chain A: R.18 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.18, A:R.18 Salt bridges: A:R.18 GTP.10: 2 residues within 4Å: Chain B: R.18 Ligands: ATP.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.18, B:R.18 Salt bridges: B:R.18 GTP.16: 2 residues within 4Å: Chain C: R.18 Ligands: ATP.17 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.18, C:R.18 Salt bridges: C:R.18 GTP.22: 2 residues within 4Å: Chain D: R.18 Ligands: ATP.23 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.18, D:R.18 Salt bridges: D:R.18 GTP.28: 2 residues within 4Å: Chain E: R.18 Ligands: ATP.29 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.18, E:R.18 Salt bridges: E:R.18 GTP.34: 2 residues within 4Å: Chain F: R.18 Ligands: ATP.35 3 PLIP interactions: 3 interactions with chain F Water bridges: F:R.18, F:R.18 Salt bridges: F:R.18 GTP.40: 2 residues within 4Å: Chain G: R.18 Ligands: ATP.41 3 PLIP interactions: 3 interactions with chain G Water bridges: G:R.18, G:R.18 Salt bridges: G:R.18 GTP.46: 2 residues within 4Å: Chain H: R.18 Ligands: ATP.47 3 PLIP interactions: 3 interactions with chain H Water bridges: H:R.18, H:R.18 Salt bridges: H:R.18 GTP.52: 2 residues within 4Å: Chain I: R.18 Ligands: ATP.53 3 PLIP interactions: 3 interactions with chain I Water bridges: I:R.18, I:R.18 Salt bridges: I:R.18 GTP.58: 2 residues within 4Å: Chain J: R.18 Ligands: ATP.59 3 PLIP interactions: 3 interactions with chain J Water bridges: J:R.18, J:R.18 Salt bridges: J:R.18 GTP.64: 2 residues within 4Å: Chain K: R.18 Ligands: ATP.65 3 PLIP interactions: 3 interactions with chain K Water bridges: K:R.18, K:R.18 Salt bridges: K:R.18 GTP.70: 2 residues within 4Å: Chain L: R.18 Ligands: ATP.71 3 PLIP interactions: 3 interactions with chain L Water bridges: L:R.18, L:R.18 Salt bridges: L:R.18

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

ATP.5: 6 residues within 4Å: Chain A: K.154, R.155, D.156, G.157 Ligands: MG.3, GTP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.156, A:D.156, A:G.157 ATP.11: 6 residues within 4Å: Chain B: K.154, R.155, D.156, G.157 Ligands: MG.9, GTP.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.156, B:D.156, B:G.157 ATP.17: 6 residues within 4Å: Chain C: K.154, R.155, D.156, G.157 Ligands: MG.15, GTP.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.156, C:D.156, C:G.157 Water bridges: C:D.156, C:D.156 ATP.23: 6 residues within 4Å: Chain D: K.154, R.155, D.156, G.157 Ligands: MG.21, GTP.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.156, D:D.156, D:G.157 Water bridges: D:D.156, D:D.156 ATP.29: 6 residues within 4Å: Chain E: K.154, R.155, D.156, G.157 Ligands: MG.27, GTP.28 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.156, E:D.156, E:G.157 Water bridges: E:D.156, E:D.156 ATP.35: 6 residues within 4Å: Chain F: K.154, R.155, D.156, G.157 Ligands: MG.33, GTP.34 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.156, F:D.156, F:G.157 ATP.41: 6 residues within 4Å: Chain G: K.154, R.155, D.156, G.157 Ligands: MG.39, GTP.40 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:D.156, G:D.156, G:G.157 Water bridges: G:D.156, G:D.156 ATP.47: 6 residues within 4Å: Chain H: K.154, R.155, D.156, G.157 Ligands: MG.45, GTP.46 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.156, H:D.156, H:G.157 ATP.53: 6 residues within 4Å: Chain I: K.154, R.155, D.156, G.157 Ligands: MG.51, GTP.52 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:D.156, I:D.156, I:G.157 Water bridges: I:D.156, I:D.156 ATP.59: 6 residues within 4Å: Chain J: K.154, R.155, D.156, G.157 Ligands: MG.57, GTP.58 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:D.156, J:D.156, J:G.157 ATP.65: 6 residues within 4Å: Chain K: K.154, R.155, D.156, G.157 Ligands: MG.63, GTP.64 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:D.156, K:D.156, K:G.157 ATP.71: 6 residues within 4Å: Chain L: K.154, R.155, D.156, G.157 Ligands: MG.69, GTP.70 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:D.156, L:D.156, L:G.157 Water bridges: L:D.156, L:D.156

12 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.6: 14 residues within 4Å: Chain A: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain B: H.76 Chain F: R.98 Ligands: MG.2, CTP.36, CTP.72 19 PLIP interactions: 16 interactions with chain A, 1 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: A:D.81 Hydrogen bonds: A:N.77, A:D.78, A:D.78, A:S.79, A:S.79, A:Y.80, A:D.81, A:D.81, A:D.81, A:R.98, A:R.98, F:R.98 Salt bridges: A:H.76, A:H.76 pi-Stacking: A:Y.80 pi-Cation interactions: A:R.98 Water bridges: E:G.74, F:R.98 CTP.12: 14 residues within 4Å: Chain A: H.76 Chain B: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain H: R.98 Ligands: MG.8, CTP.48, CTP.54 19 PLIP interactions: 16 interactions with chain B, 1 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: B:D.81 Hydrogen bonds: B:N.77, B:D.78, B:D.78, B:S.79, B:S.79, B:Y.80, B:D.81, B:D.81, B:D.81, B:R.98, B:R.98, H:R.98 Salt bridges: B:H.76, B:H.76 pi-Stacking: B:Y.80 pi-Cation interactions: B:R.98 Water bridges: G:G.74, H:R.98 CTP.18: 14 residues within 4Å: Chain C: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain D: H.76 Chain G: R.98 Ligands: MG.14, CTP.42, CTP.66 17 PLIP interactions: 14 interactions with chain C, 2 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: C:D.81 Hydrogen bonds: C:N.77, C:D.78, C:S.79, C:S.79, C:Y.80, C:D.81, C:D.81, C:R.98, C:R.98, G:R.98 Salt bridges: C:H.76, C:H.76 pi-Stacking: C:Y.80 pi-Cation interactions: C:R.98 Water bridges: G:R.98, H:G.74 CTP.24: 14 residues within 4Å: Chain C: H.76 Chain D: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain E: R.98 Ligands: MG.20, CTP.30, CTP.60 17 PLIP interactions: 14 interactions with chain D, 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: D:D.81 Hydrogen bonds: D:N.77, D:D.78, D:S.79, D:S.79, D:Y.80, D:D.81, D:D.81, D:R.98, D:R.98, E:R.98 Salt bridges: D:H.76, D:H.76 pi-Stacking: D:Y.80 pi-Cation interactions: D:R.98 Water bridges: E:R.98, F:G.74 CTP.30: 14 residues within 4Å: Chain E: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain F: H.76 Chain J: R.98 Ligands: CTP.24, MG.26, CTP.60 18 PLIP interactions: 1 interactions with chain I, 2 interactions with chain J, 15 interactions with chain E Water bridges: I:G.74, J:R.98 Hydrogen bonds: J:R.98, E:N.77, E:D.78, E:S.79, E:S.79, E:Y.80, E:D.81, E:D.81, E:D.81, E:R.98, E:R.98 Hydrophobic interactions: E:D.81 Salt bridges: E:H.76, E:H.76 pi-Stacking: E:Y.80 pi-Cation interactions: E:R.98 CTP.36: 14 residues within 4Å: Chain E: H.76 Chain F: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain L: R.98 Ligands: CTP.6, MG.32, CTP.72 18 PLIP interactions: 1 interactions with chain K, 15 interactions with chain F, 2 interactions with chain L Water bridges: K:G.74, L:R.98 Hydrophobic interactions: F:D.81 Hydrogen bonds: F:N.77, F:D.78, F:D.78, F:S.79, F:S.79, F:Y.80, F:D.81, F:D.81, F:R.98, F:R.98, L:R.98 Salt bridges: F:H.76, F:H.76 pi-Stacking: F:Y.80 pi-Cation interactions: F:R.98 CTP.42: 14 residues within 4Å: Chain G: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain H: H.76 Chain K: R.98 Ligands: CTP.18, MG.38, CTP.66 18 PLIP interactions: 1 interactions with chain L, 15 interactions with chain G, 2 interactions with chain K Water bridges: L:G.74, K:R.98 Hydrophobic interactions: G:D.81 Hydrogen bonds: G:N.77, G:D.78, G:S.79, G:S.79, G:Y.80, G:D.81, G:D.81, G:D.81, G:R.98, G:R.98, K:R.98 Salt bridges: G:H.76, G:H.76 pi-Stacking: G:Y.80 pi-Cation interactions: G:R.98 CTP.48: 14 residues within 4Å: Chain G: H.76 Chain H: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain I: R.98 Ligands: CTP.12, MG.44, CTP.54 18 PLIP interactions: 15 interactions with chain H, 2 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: H:D.81 Hydrogen bonds: H:N.77, H:D.78, H:D.78, H:S.79, H:S.79, H:Y.80, H:D.81, H:D.81, H:R.98, H:R.98, I:R.98 Salt bridges: H:H.76, H:H.76 pi-Stacking: H:Y.80 pi-Cation interactions: H:R.98 Water bridges: I:R.98, J:G.74 CTP.54: 14 residues within 4Å: Chain B: R.98 Chain I: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain J: H.76 Ligands: CTP.12, CTP.48, MG.50 18 PLIP interactions: 15 interactions with chain I, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: I:D.81 Hydrogen bonds: I:N.77, I:D.78, I:D.78, I:S.79, I:S.79, I:Y.80, I:D.81, I:D.81, I:R.98, I:R.98, B:R.98 Salt bridges: I:H.76, I:H.76 pi-Stacking: I:Y.80 pi-Cation interactions: I:R.98 Water bridges: B:R.98, A:G.74 CTP.60: 14 residues within 4Å: Chain D: R.98 Chain I: H.76 Chain J: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Ligands: CTP.24, CTP.30, MG.56 18 PLIP interactions: 15 interactions with chain J, 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: J:D.81 Hydrogen bonds: J:N.77, J:D.78, J:S.79, J:S.79, J:Y.80, J:D.81, J:D.81, J:D.81, J:R.98, J:R.98, D:R.98 Salt bridges: J:H.76, J:H.76 pi-Stacking: J:Y.80 pi-Cation interactions: J:R.98 Water bridges: C:G.74, D:R.98 CTP.66: 14 residues within 4Å: Chain C: R.98 Chain K: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Chain L: H.76 Ligands: CTP.18, CTP.42, MG.62 18 PLIP interactions: 15 interactions with chain K, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: K:D.81 Hydrogen bonds: K:N.77, K:D.78, K:S.79, K:S.79, K:Y.80, K:D.81, K:D.81, K:D.81, K:R.98, K:R.98, C:R.98 Salt bridges: K:H.76, K:H.76 pi-Stacking: K:Y.80 pi-Cation interactions: K:R.98 Water bridges: C:R.98, D:G.74 CTP.72: 14 residues within 4Å: Chain A: R.98 Chain K: H.76 Chain L: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, R.98 Ligands: CTP.6, CTP.36, MG.68 18 PLIP interactions: 15 interactions with chain L, 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: L:D.81 Hydrogen bonds: L:N.77, L:D.78, L:D.78, L:S.79, L:S.79, L:Y.80, L:D.81, L:D.81, L:R.98, L:R.98, A:R.98 Salt bridges: L:H.76, L:H.76 pi-Stacking: L:Y.80 pi-Cation interactions: L:R.98 Water bridges: B:G.74, A:R.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, S. et al., Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells. ACS Nano (2017)

Release Date

2017-02-15

Peptides

Polyhedrin: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Polyhedrin

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