SMTL ID : 5chb.1

Crystal structure of nvPizza2-S16H58 coordinating a CdCl2 nanocrystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-hexamer

Ligands

12 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.1: 3 residues within 4Å: Chain A: H.54 Chain B: H.54 Chain C: H.54 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.54, C:H.54, A:H.54, H2O.3, H2O.3, H2O.3 CD.2: 6 residues within 4Å: Chain B: H.69 Chain D: H.69 Ligands: CL.5, CL.6, CL.7, CL.13 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.69, B:H.69 CD.3: 9 residues within 4Å: Chain B: H.27 Chain E: H.27 Ligands: CD.4, CL.5, CL.6, CD.16, CD.17, CL.18, CL.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Metal complexes: B:H.27, E:H.27 CD.4: 9 residues within 4Å: Ligands: CD.3, CL.5, CL.7, CL.12, CD.16, CD.17, CL.18, CL.20, CL.25 No protein-ligand interaction detected (PLIP) CD.9: 6 residues within 4Å: Chain C: H.27 Chain D: H.27 Ligands: CL.7, CL.11, CL.12, CL.13 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.27, C:H.27 CD.10: 7 residues within 4Å: Chain C: H.69 Chain F: H.69 Ligands: CL.11, CL.12, CD.23, CL.24, CL.25 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Metal complexes: C:H.69, F:H.69 CD.14: 3 residues within 4Å: Chain D: H.54 Chain E: H.54 Chain F: H.54 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: D:H.54, F:H.54, E:H.54, H2O.9, H2O.9, H2O.9 CD.15: 6 residues within 4Å: Chain A: H.69 Chain E: H.69 Ligands: CL.18, CL.19, CL.20, CL.26 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Metal complexes: E:H.69, A:H.69 CD.16: 9 residues within 4Å: Chain B: H.27 Chain E: H.27 Ligands: CD.3, CD.4, CL.5, CL.6, CD.17, CL.18, CL.19 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Metal complexes: B:H.27, E:H.27 CD.17: 9 residues within 4Å: Ligands: CD.3, CD.4, CL.5, CL.7, CL.12, CD.16, CL.18, CL.20, CL.25 No protein-ligand interaction detected (PLIP) CD.22: 6 residues within 4Å: Chain A: H.27 Chain F: H.27 Ligands: CL.20, CL.24, CL.25, CL.26 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Metal complexes: F:H.27, A:H.27 CD.23: 7 residues within 4Å: Chain C: H.69 Chain F: H.69 Ligands: CD.10, CL.11, CL.12, CL.24, CL.25 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Metal complexes: C:H.69, F:H.69

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

CL.5: 16 residues within 4Å: Chain D: H.54, H.69 Chain E: H.27, H.54 Ligands: CD.2, CD.3, CD.4, CL.6, CL.7, CL.12, CL.13, CD.16, CD.17, CL.18, CL.19, CL.20 Ligand excluded by PLIP CL.6: 11 residues within 4Å: Chain B: H.27, H.54, H.69 Chain D: H.69 Chain E: H.27 Ligands: CD.2, CD.3, CL.5, CL.7, CD.16, CL.18 Ligand excluded by PLIP CL.7: 14 residues within 4Å: Chain B: H.54, H.69 Chain C: H.27 Ligands: CD.2, CD.4, CL.5, CL.6, CD.9, CL.11, CL.12, CL.13, CD.17, CL.18, CL.25 Ligand excluded by PLIP CL.11: 11 residues within 4Å: Chain C: H.27, H.54, H.69 Chain D: H.27 Chain F: H.69 Ligands: CL.7, CD.9, CD.10, CL.12, CD.23, CL.25 Ligand excluded by PLIP CL.12: 15 residues within 4Å: Chain D: H.27 Chain F: H.54, H.69 Ligands: CD.4, CL.5, CL.7, CD.9, CD.10, CL.11, CL.13, CD.17, CL.20, CD.23, CL.24, CL.25 Ligand excluded by PLIP CL.13: 10 residues within 4Å: Chain B: H.69 Chain C: H.27 Chain D: H.27, H.54, H.69 Ligands: CD.2, CL.5, CL.7, CD.9, CL.12 Ligand excluded by PLIP CL.18: 16 residues within 4Å: Chain A: H.54, H.69 Chain B: H.27, H.54 Ligands: CD.3, CD.4, CL.5, CL.6, CL.7, CD.15, CD.16, CD.17, CL.19, CL.20, CL.25, CL.26 Ligand excluded by PLIP CL.19: 11 residues within 4Å: Chain A: H.69 Chain B: H.27 Chain E: H.27, H.54, H.69 Ligands: CD.3, CL.5, CD.15, CD.16, CL.18, CL.20 Ligand excluded by PLIP CL.20: 14 residues within 4Å: Chain E: H.54, H.69 Chain F: H.27 Ligands: CD.4, CL.5, CL.12, CD.15, CD.17, CL.18, CL.19, CD.22, CL.24, CL.25, CL.26 Ligand excluded by PLIP CL.24: 11 residues within 4Å: Chain A: H.27 Chain C: H.69 Chain F: H.27, H.54, H.69 Ligands: CD.10, CL.12, CL.20, CD.22, CD.23, CL.25 Ligand excluded by PLIP CL.25: 15 residues within 4Å: Chain A: H.27 Chain C: H.54, H.69 Ligands: CD.4, CL.7, CD.10, CL.11, CL.12, CD.17, CL.18, CL.20, CD.22, CD.23, CL.24, CL.26 Ligand excluded by PLIP CL.26: 10 residues within 4Å: Chain A: H.27, H.54, H.69 Chain E: H.69 Chain F: H.27 Ligands: CD.15, CL.18, CL.20, CD.22, CL.25 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 9 residues within 4Å: Chain A: S.12, G.13, G.55 Chain B: S.12, G.13, G.55 Chain C: S.12, G.13, G.55 12 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C, 4 interactions with chain A Water bridges: B:V.14, B:V.14, B:V.56, B:V.56, B:V.56, C:V.14, C:V.14, C:V.56, A:V.14, A:V.14, A:V.14, A:V.56 SO4.21: 9 residues within 4Å: Chain D: S.12, G.13, G.55 Chain E: S.12, G.13, G.55 Chain F: S.12, G.13, G.55 12 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D, 3 interactions with chain F Water bridges: E:V.14, E:V.14, E:V.56, E:V.56, E:V.56, D:V.14, D:V.14, D:V.14, D:V.56, F:V.14, F:V.14, F:V.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Voet, A.R.D. et al., Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-07-22

Peptides

nvPizza2-S16H58: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

nvPizza2-S16H58