SMTL ID : 5yha.1

Crystal structure of Pd(allyl)/Wild Type Polyhedra

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: S.30, L.31 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: S.30, L.31 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain C: S.30, L.31 Ligand excluded by PLIP

9 x PLL: Palladium(II) allyl complex(Non-covalent)

PLL.2: 5 residues within 4Å: Chain A: R.209, C.211 Chain C: T.64 Ligands: PLL.3, PD.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.211 PLL.3: 5 residues within 4Å: Chain A: I.51, E.63, C.211 Ligands: PLL.2, PD.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.211 PLL.4: 3 residues within 4Å: Chain A: R.155, H.238, S.239 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.238, H2O.1 PLL.12: 5 residues within 4Å: Chain A: T.64 Chain B: R.209, C.211 Ligands: PLL.13, PD.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.211 PLL.13: 5 residues within 4Å: Chain B: I.51, E.63, C.211 Ligands: PLL.12, PD.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.211 PLL.14: 3 residues within 4Å: Chain B: R.155, H.238, S.239 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.238, H2O.5 PLL.22: 5 residues within 4Å: Chain B: T.64 Chain C: R.209, C.211 Ligands: PLL.23, PD.26 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.211 PLL.23: 5 residues within 4Å: Chain C: I.51, E.63, C.211 Ligands: PLL.22, PD.26 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.211 PLL.24: 3 residues within 4Å: Chain C: R.155, H.238, S.239 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.238, H2O.9

15 x PD: PALLADIUM ION(Non-covalent)

PD.5: 1 residues within 4Å: Chain A: H.76 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 PD.6: 4 residues within 4Å: Chain A: C.211 Chain C: K.66 Ligands: PLL.2, PLL.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.211 PD.7: 1 residues within 4Å: Chain A: H.170 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.170 PD.8: 5 residues within 4Å: Chain A: K.58, C.204 Chain B: C.204 Ligands: PD.18, PD.28 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.204, H2O.5 PD.9: 1 residues within 4Å: Chain A: H.238 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.238 PD.15: 1 residues within 4Å: Chain B: H.76 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.76 PD.16: 4 residues within 4Å: Chain A: K.66 Chain B: C.211 Ligands: PLL.12, PLL.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.211 PD.17: 1 residues within 4Å: Chain B: H.170 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.170 PD.18: 5 residues within 4Å: Chain B: K.58, C.204 Chain C: C.204 Ligands: PD.8, PD.28 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.204, H2O.9 PD.19: 1 residues within 4Å: Chain B: H.238 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.238 PD.25: 1 residues within 4Å: Chain C: H.76 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.76 PD.26: 4 residues within 4Å: Chain B: K.66 Chain C: C.211 Ligands: PLL.22, PLL.23 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.211 PD.27: 1 residues within 4Å: Chain C: H.170 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.170 PD.28: 5 residues within 4Å: Chain A: C.204 Chain C: K.58, C.204 Ligands: PD.8, PD.18 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.204, H2O.13 PD.29: 1 residues within 4Å: Chain C: H.238 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.238

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

EDO.10: 3 residues within 4Å: Chain A: G.46, A.216, E.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.46, A:E.217 Water bridges: A:L.218 EDO.20: 3 residues within 4Å: Chain B: G.46, A.216, E.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.46, B:E.217 Water bridges: B:L.218 EDO.30: 3 residues within 4Å: Chain C: G.46, A.216, E.217 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.46, C:E.217 Water bridges: C:L.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, S. et al., Structure of in cell protein crystals containing organometallic complexes. Phys Chem Chem Phys (2018)

Release Date

2017-11-29

Peptides

Polyhedrin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Polyhedrin

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