5HZU: Dronpa-Ni2+

Crystal structure of Dronpa-Ni2+. Determined by X-ray diffraction at 1.89 Å resolution. Released 15 Mar 2017.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Echinophyllia sp. SC22
Chains: 12
Atoms: 22,735
Mol. weight: 297.32 kDa
Ligands: NI
Released: 15 Mar 2017

Explore 5HZU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HZU contains 72 α-helices and 156 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and D: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	1
β-strand	21-32	12	1
α-helix	33-35	3
β-strand	37-46	10	1
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	1
α-helix	78-81	4
β-strand	87-95	9	1
β-strand	100-110	11	1
β-strand	113-123	11	1
β-strand	136-139	4	1
α-helix	140-141	2
β-strand	142-149	8	1
β-strand	152-163	12	1
β-strand	168-179	12	1
α-helix	184-187	4
β-strand	189-200	12	1
β-strand	206-216	11	1

Chains B, E, H, I, J, K and L: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	2
β-strand	21-32	12	2
β-strand	37-46	10	2
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	2
α-helix	78-81	4
β-strand	87-95	9	2
β-strand	100-110	11	2
β-strand	113-123	11	2
β-strand	136-139	4	2
α-helix	140-141	2
β-strand	142-149	8	2
β-strand	152-163	12	2
β-strand	168-179	12	2
α-helix	184-187	4
β-strand	189-200	12	2
β-strand	206-216	11	2

Chains C and G: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	3
β-strand	21-32	12	3
β-strand	37-46	10	3
α-helix	48	1
α-helix	50	1
α-helix	55-58	4
β-strand	70	1	3
α-helix	80-82	3
β-strand	87-95	9	3
β-strand	100-110	11	3
β-strand	113-123	11	3
β-strand	136-139	4	3
α-helix	140-141	2
β-strand	142-149	8	3
β-strand	152-163	12	3
β-strand	168-179	12	3
α-helix	184-187	4
β-strand	189-200	12	3
β-strand	206-216	11	3

Chain F: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-18	11	6
β-strand	21-32	12	6
β-strand	37-46	10	6
α-helix	55-58	4
β-strand	70	1	6
α-helix	78-82	5
β-strand	87-95	9	6
β-strand	100-110	11	6
β-strand	113-123	11	6
β-strand	136-139	4	6
α-helix	140-141	2
β-strand	142-149	8	6
β-strand	152-163	12	6
β-strand	168-179	12	6
α-helix	184-187	4
β-strand	189-200	12	6
β-strand	206-216	11	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fluorescent protein Dronpa	A, B, C, D, E, F, G, H, I, J, K, L	protein	215	Echinophyllia sp. SC22	Q5TLG6 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>5HZU_1 Fluorescent protein Dronpa (chains A, B, C, D, E, F, G, H, I, J, K, L)
SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVF
XNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGV
NFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVV
QLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	25

Primary citation

Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development. Kim, I.J., Kim, S., Park, J. et al. FEBS Lett (2016) 590:2982-2990. DOI 10.1002/1873-3468.12316 · PubMed

Other PDB entries of the same protein (UniProt Q5TLG6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2IE2 1.7 Å, The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein
7RRH 1.75 Å, Crystal structure of fast switching R66M/M159T mutant of fluorescent protein Dronpa…
2Z1O 1.75 Å, Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
2GX2 1.8 Å, Crystal structural and functional analysis of GFP-like fluorescent protein Dronpa
2IOV 1.8 Å, Bright-state structure of the reversibly switchable fluorescent protein Dronpa
2Z6Z 1.8 Å, Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state
6MYB 1.9 Å, Room-temperature structure of deuterated Tetdron (isomorph 1)
2GX0 1.9 Å, Crystal structural and functional analysis of GFP-like fluorescent protein
7RRK 1.93 Å, Crystal structure of fast switching M159E mutant of fluorescent protein Dronpa (Dronpa2)
2POX 1.95 Å, Dark state structure of the reversibly switchable fluorescent protein Dronpa
4EMQ 1.95 Å, Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4
4HQ8 1.95 Å, Crystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the…

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