SMTL ID : 5axu.1

Crystal Structure of Cypovirus Polyhedra R13A Mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-12-mer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ATP.14 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: ATP.20 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Ligands: ATP.26 No protein-ligand interaction detected (PLIP) MG.31: 1 residues within 4Å: Ligands: ATP.32 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Ligands: ATP.38 No protein-ligand interaction detected (PLIP) MG.43: 1 residues within 4Å: Ligands: ATP.44 No protein-ligand interaction detected (PLIP) MG.49: 1 residues within 4Å: Ligands: ATP.50 No protein-ligand interaction detected (PLIP) MG.55: 1 residues within 4Å: Ligands: ATP.56 No protein-ligand interaction detected (PLIP) MG.61: 1 residues within 4Å: Ligands: ATP.62 No protein-ligand interaction detected (PLIP) MG.67: 1 residues within 4Å: Ligands: ATP.68 No protein-ligand interaction detected (PLIP)

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

ATP.2: 8 residues within 4Å: Chain A: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.25, A:Y.162, A:K.184 Water bridges: A:V.117, A:Y.162 Salt bridges: A:K.152, A:K.152, A:K.152, A:K.154, A:K.154, A:K.154 ATP.8: 8 residues within 4Å: Chain B: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.25, B:Y.162, B:K.184 Water bridges: B:V.117, B:Y.162 Salt bridges: B:K.152, B:K.152, B:K.152, B:K.154, B:K.154, B:K.154 ATP.14: 8 residues within 4Å: Chain C: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.162, C:K.184 Water bridges: C:V.117, C:Y.162 Salt bridges: C:K.152, C:K.152, C:K.152, C:K.154, C:K.154, C:K.154 ATP.20: 8 residues within 4Å: Chain D: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Y.162, D:K.184 Water bridges: D:V.117, D:Y.162 Salt bridges: D:K.152, D:K.152, D:K.152, D:K.154, D:K.154, D:K.154 ATP.26: 8 residues within 4Å: Chain E: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.25 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Y.25, E:Y.162, E:K.184 Water bridges: E:V.117, E:Y.162 Salt bridges: E:K.152, E:K.152, E:K.152, E:K.154, E:K.154, E:K.154 ATP.32: 8 residues within 4Å: Chain F: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.31 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Y.162, F:K.184 Water bridges: F:V.117, F:Y.162 Salt bridges: F:K.152, F:K.152, F:K.152, F:K.154, F:K.154, F:K.154 ATP.38: 8 residues within 4Å: Chain G: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.37 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:Y.25, G:Y.162, G:K.184 Water bridges: G:V.117, G:Y.162 Salt bridges: G:K.152, G:K.152, G:K.152, G:K.154, G:K.154, G:K.154 ATP.44: 8 residues within 4Å: Chain H: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.43 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:Y.162, H:K.184 Water bridges: H:V.117, H:Y.162 Salt bridges: H:K.152, H:K.152, H:K.152, H:K.154, H:K.154, H:K.154 ATP.50: 8 residues within 4Å: Chain I: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.49 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:Y.25, I:Y.162, I:K.184 Water bridges: I:V.117, I:Y.162 Salt bridges: I:K.152, I:K.152, I:K.152, I:K.154, I:K.154, I:K.154 ATP.56: 8 residues within 4Å: Chain J: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.55 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:Y.162, J:K.184 Water bridges: J:V.117, J:Y.162 Salt bridges: J:K.152, J:K.152, J:K.152, J:K.154, J:K.154, J:K.154 ATP.62: 8 residues within 4Å: Chain K: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.61 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:Y.162, K:K.184 Water bridges: K:V.117, K:Y.162 Salt bridges: K:K.152, K:K.152, K:K.152, K:K.154, K:K.154, K:K.154 ATP.68: 8 residues within 4Å: Chain L: Y.25, K.152, K.154, G.157, I.159, Y.162, K.184 Ligands: MG.67 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:Y.25, L:Y.162, L:K.184 Water bridges: L:V.117, L:Y.162 Salt bridges: L:K.152, L:K.152, L:K.152, L:K.154, L:K.154, L:K.154

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

CTP.3: 14 residues within 4Å: Chain A: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Chain B: H.76 Chain J: R.98 Ligands: CTP.39, CTP.57 16 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A, 2 interactions with chain J Salt bridges: B:H.76, A:H.76, A:H.76 Hydrogen bonds: A:N.77, A:D.78, A:S.79, A:Y.80, A:D.81, A:D.81, A:R.98, A:R.98, J:R.98, J:R.98 Water bridges: A:N.77 pi-Stacking: A:Y.80 pi-Cation interactions: A:R.98 CTP.9: 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, A.97, R.98 Chain K: R.98 Ligands: CTP.27, CTP.63 16 PLIP interactions: 13 interactions with chain B, 2 interactions with chain K, 1 interactions with chain A Hydrogen bonds: B:N.77, B:D.78, B:S.79, B:Y.80, B:D.81, B:D.81, B:R.98, B:R.98, K:R.98, K:R.98 Water bridges: B:N.77 Salt bridges: B:H.76, B:H.76, A:H.76 pi-Stacking: B:Y.80 pi-Cation interactions: B:R.98 CTP.15: 14 residues within 4Å: Chain C: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Chain D: H.76 Chain I: R.98 Ligands: CTP.33, CTP.51 18 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D, 2 interactions with chain I Hydrogen bonds: C:N.77, C:D.78, C:D.78, C:S.79, C:Y.80, C:D.81, C:D.81, C:D.81, C:R.98, C:R.98, I:R.98, I:R.98 Water bridges: C:N.77 Salt bridges: C:H.76, C:H.76, D:H.76 pi-Stacking: C:Y.80 pi-Cation interactions: C:R.98 CTP.21: 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, A.97, R.98 Chain L: R.98 Ligands: CTP.45, CTP.69 18 PLIP interactions: 15 interactions with chain D, 2 interactions with chain L, 1 interactions with chain C Hydrogen bonds: D:N.77, D:D.78, D:D.78, D:S.79, D:Y.80, D:D.81, D:D.81, D:D.81, D:R.98, D:R.98, L:R.98, L:R.98 Water bridges: D:N.77 Salt bridges: D:H.76, D:H.76, C:H.76 pi-Stacking: D:Y.80 pi-Cation interactions: D:R.98 CTP.27: 14 residues within 4Å: Chain B: R.98 Chain E: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Chain F: H.76 Ligands: CTP.9, CTP.63 17 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F, 2 interactions with chain B Hydrogen bonds: E:N.77, E:D.78, E:S.79, E:Y.80, E:D.81, E:D.81, E:D.81, E:R.98, E:R.98, B:R.98, B:R.98 Water bridges: E:N.77 Salt bridges: E:H.76, E:H.76, F:H.76 pi-Stacking: E:Y.80 pi-Cation interactions: E:R.98 CTP.33: 14 residues within 4Å: Chain C: R.98 Chain E: H.76 Chain F: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Ligands: CTP.15, CTP.51 17 PLIP interactions: 14 interactions with chain F, 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: F:N.77, F:D.78, F:D.78, F:S.79, F:Y.80, F:D.81, F:D.81, F:R.98, F:R.98, C:R.98, C:R.98 Water bridges: F:N.77 Salt bridges: F:H.76, F:H.76, E:H.76 pi-Stacking: F:Y.80 pi-Cation interactions: F:R.98 CTP.39: 14 residues within 4Å: Chain A: R.98 Chain G: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Chain H: H.76 Ligands: CTP.3, CTP.57 17 PLIP interactions: 14 interactions with chain G, 2 interactions with chain A, 1 interactions with chain H Hydrogen bonds: G:N.77, G:D.78, G:S.79, G:Y.80, G:D.81, G:D.81, G:D.81, G:R.98, G:R.98, A:R.98, A:R.98 Water bridges: G:N.77 Salt bridges: G:H.76, G:H.76, H:H.76 pi-Stacking: G:Y.80 pi-Cation interactions: G:R.98 CTP.45: 14 residues within 4Å: Chain D: R.98 Chain G: H.76 Chain H: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Ligands: CTP.21, CTP.69 17 PLIP interactions: 2 interactions with chain D, 1 interactions with chain G, 14 interactions with chain H Hydrogen bonds: D:R.98, D:R.98, H:N.77, H:D.78, H:D.78, H:S.79, H:Y.80, H:D.81, H:D.81, H:R.98, H:R.98 Salt bridges: G:H.76, H:H.76, H:H.76 Water bridges: H:N.77 pi-Stacking: H:Y.80 pi-Cation interactions: H:R.98 CTP.51: 14 residues within 4Å: Chain F: R.98 Chain I: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Chain J: H.76 Ligands: CTP.15, CTP.33 17 PLIP interactions: 14 interactions with chain I, 2 interactions with chain F, 1 interactions with chain J Hydrogen bonds: I:N.77, I:D.78, I:D.78, I:S.79, I:Y.80, I:D.81, I:D.81, I:R.98, I:R.98, F:R.98, F:R.98 Water bridges: I:N.77 Salt bridges: I:H.76, I:H.76, J:H.76 pi-Stacking: I:Y.80 pi-Cation interactions: I:R.98 CTP.57: 14 residues within 4Å: Chain G: R.98 Chain I: H.76 Chain J: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Ligands: CTP.3, CTP.39 17 PLIP interactions: 2 interactions with chain G, 1 interactions with chain I, 14 interactions with chain J Hydrogen bonds: G:R.98, G:R.98, J:N.77, J:D.78, J:S.79, J:Y.80, J:D.81, J:D.81, J:D.81, J:R.98, J:R.98 Salt bridges: I:H.76, J:H.76, J:H.76 Water bridges: J:N.77 pi-Stacking: J:Y.80 pi-Cation interactions: J:R.98 CTP.63: 14 residues within 4Å: Chain E: R.98 Chain K: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Chain L: H.76 Ligands: CTP.9, CTP.27 17 PLIP interactions: 14 interactions with chain K, 1 interactions with chain L, 2 interactions with chain E Hydrogen bonds: K:N.77, K:D.78, K:S.79, K:Y.80, K:D.81, K:D.81, K:D.81, K:R.98, K:R.98, E:R.98, E:R.98 Water bridges: K:N.77 Salt bridges: K:H.76, K:H.76, L:H.76 pi-Stacking: K:Y.80 pi-Cation interactions: K:R.98 CTP.69: 14 residues within 4Å: Chain H: R.98 Chain K: H.76 Chain L: H.76, N.77, D.78, S.79, Y.80, D.81, E.84, D.96, A.97, R.98 Ligands: CTP.21, CTP.45 17 PLIP interactions: 14 interactions with chain L, 2 interactions with chain H, 1 interactions with chain K Hydrogen bonds: L:N.77, L:D.78, L:D.78, L:S.79, L:Y.80, L:D.81, L:D.81, L:R.98, L:R.98, H:R.98, H:R.98 Water bridges: L:N.77 Salt bridges: L:H.76, L:H.76, K:H.76 pi-Stacking: L:Y.80 pi-Cation interactions: L:R.98

36 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: N.28, W.38, S.114, P.115, V.160, P.231 Chain E: Q.138 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: E.23, Y.27 Chain E: R.139 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: N.28, W.38, S.114, P.115, V.160, P.231 Chain G: Q.138 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: E.23, Y.27 Chain G: R.139 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain C: N.28, W.38, S.114, P.115, V.160, P.231 Chain H: Q.138 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: E.23, Y.27 Chain H: R.139 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain D: N.28, W.38, S.114, P.115, V.160, P.231 Chain F: Q.138 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain D: E.23, Y.27 Chain F: R.139 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain E: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain E: N.28, W.38, S.114, P.115, V.160, P.231 Chain I: Q.138 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain E: E.23, Y.27 Chain I: R.139 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain F: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain F: N.28, W.38, S.114, P.115, V.160, P.231 Chain K: Q.138 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain F: E.23, Y.27 Chain K: R.139 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain G: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain G: N.28, W.38, S.114, P.115, V.160, P.231 Chain L: Q.138 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain G: E.23, Y.27 Chain L: R.139 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain H: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain H: N.28, W.38, S.114, P.115, V.160, P.231 Chain J: Q.138 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain H: E.23, Y.27 Chain J: R.139 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain I: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain A: Q.138 Chain I: N.28, W.38, S.114, P.115, V.160, P.231 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain A: R.139 Chain I: E.23, Y.27 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain J: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain C: Q.138 Chain J: N.28, W.38, S.114, P.115, V.160, P.231 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain C: R.139 Chain J: E.23, Y.27 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain K: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain D: Q.138 Chain K: N.28, W.38, S.114, P.115, V.160, P.231 Ligand excluded by PLIP EDO.66: 3 residues within 4Å: Chain D: R.139 Chain K: E.23, Y.27 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain L: Y.42, E.217, I.235 Ligand excluded by PLIP EDO.71: 7 residues within 4Å: Chain B: Q.138 Chain L: N.28, W.38, S.114, P.115, V.160, P.231 Ligand excluded by PLIP EDO.72: 3 residues within 4Å: Chain B: R.139 Chain L: E.23, Y.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, S. et al., Design of Enzyme-Encapsulated Protein Containers by In Vivo Crystal Engineering. Adv. Mater. Weinheim (2015)

Release Date

2015-11-11

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