SMTL ID : 5bu7.1

Crystal structure of an engineered protein that forms nanotubes with tunable diameters

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 17 residues within 4Å: Chain A: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:L.10, A:L.14, A:P.45, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106 pi-Stacking: A:H.102 pi-Cation interactions: A:R.106, A:R.106 Metal complexes: A:H.102 HEM.6: 15 residues within 4Å: Chain B: E.4, M.7, E.8, L.10, N.11, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:M.7, B:L.10, B:L.10, B:N.11, B:P.45, B:F.65, B:F.65, B:F.65, B:R.106 Hydrogen bonds: B:E.4 pi-Stacking: B:H.102, B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEM.10: 17 residues within 4Å: Chain C: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:L.10, C:L.14, C:P.45, C:F.65, C:F.65, C:F.65, C:L.68, C:R.106 Hydrogen bonds: C:E.4 pi-Stacking: C:H.102 pi-Cation interactions: C:R.106, C:R.106 Metal complexes: C:H.102 HEM.15: 15 residues within 4Å: Chain D: E.4, M.7, E.8, L.10, N.11, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:M.7, D:L.10, D:L.10, D:N.11, D:P.45, D:F.65, D:F.65, D:F.65, D:R.106 pi-Stacking: D:H.102, D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102

14 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: A.1, D.39, K.42 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.1, A:D.39, A:D.39 ZN.3: 2 residues within 4Å: Chain A: E.8, D.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.8, A:D.12, A:D.12 ZN.4: 5 residues within 4Å: Chain A: H.73, H.77 Chain B: H.63, I.67 Chain C: D.74 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.74, C:D.74, A:H.73, A:H.77, B:H.63 ZN.5: 5 residues within 4Å: Chain A: E.27, K.28, E.31 Chain B: D.54, H.59 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.59, A:E.27, A:E.31, A:E.31, H2O.2 ZN.7: 4 residues within 4Å: Chain A: H.63 Chain B: H.73, H.77 Chain D: D.74 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 interactions with chain A Metal complexes: B:H.73, B:H.77, D:D.74, D:D.74, A:H.63 ZN.8: 2 residues within 4Å: Chain B: A.1, D.39 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.1, B:D.39, H2O.2 ZN.9: 4 residues within 4Å: Chain A: D.54, H.59 Chain B: E.27, E.31 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.27, B:E.31, B:E.31, A:H.59, H2O.1 ZN.11: 3 residues within 4Å: Chain C: A.1, D.39, K.42 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.1, C:D.39, C:D.39 ZN.12: 2 residues within 4Å: Chain C: E.8, D.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.8, C:D.12, C:D.12 ZN.13: 5 residues within 4Å: Chain A: D.74 Chain C: H.73, H.77 Chain D: H.63, I.67 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 interactions with chain A Metal complexes: C:H.73, C:H.77, D:H.63, A:D.74, A:D.74 ZN.14: 5 residues within 4Å: Chain C: E.27, K.28, E.31 Chain D: D.54, H.59 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.59, C:E.27, C:E.31, C:E.31, H2O.4 ZN.16: 4 residues within 4Å: Chain B: D.74 Chain C: H.63 Chain D: H.73, H.77 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 interactions with chain B Metal complexes: C:H.63, D:H.73, D:H.77, B:D.74, B:D.74 ZN.17: 2 residues within 4Å: Chain D: A.1, D.39 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.1, D:D.39, H2O.4 ZN.18: 4 residues within 4Å: Chain C: D.54, H.59 Chain D: E.27, E.31 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.27, D:E.31, D:E.31, C:H.59, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brodin, J.D. et al., Designed, Helical Protein Nanotubes with Tunable Diameters from a Single Building Block. To be Published

Release Date

2016-06-08

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Soluble cytochrome b562