MolNFT v1 · #121584 · protein

Crystal structure of dronpa-CU2+

5HZT · Fluorescent protein dronpa: “Crystal structure of dronpa-CU2+”. X-ray diffraction, 2 ligands (GYS, CU), 20 pockets (best druggability 0.83). MolNFT v1 #121584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HZT
Type: protein
Length: 2,505 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein dronpa
UniProt: Q5TLG6
Ligands: GYS, CU
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 4% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein dronpa	protein	192	2% helix, 64% strand	Q5TLG6
B	Fluorescent protein dronpa	protein	209	4% helix, 59% strand	Q5TLG6
C, G	Fluorescent protein dronpa	protein	213	4% helix, 58% strand	Q5TLG6
D, E, H	Fluorescent protein dronpa	protein	214	4% helix, 58% strand	Q5TLG6
F, L	Fluorescent protein dronpa	protein	213	4% helix, 58% strand	Q5TLG6
I	Fluorescent protein dronpa	protein	212	4% helix, 58% strand	Q5TLG6
J	Fluorescent protein dronpa	protein	210	4% helix, 59% strand	Q5TLG6
K	Fluorescent protein dronpa	protein	188	2% helix, 63% strand	Q5TLG6

Ligands and binding sites

GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
CU · Copper (II) ion · metal · 24 copies · chains A, J, B, C, D, E, F, G, H, I, K, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.83	0.85	91	empty
2	948	0.83	0.85	92	empty
3	1123	0.81	0.83	94	empty
4	112	0.77	0.97	29	GYS
5	102	0.77	0.97	28	GYS

Interfaces

19 interfaces between chains.

D–E · 941 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 898 Å² buried · 20 hydrogen bonds · protein-protein
A–L · 884 Å² buried · 17 hydrogen bonds · protein-protein
F–G · 879 Å² buried · 17 hydrogen bonds · protein-protein
D–I · 869 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 cofactor (chromophore).

Compared structures

5HZT · Crystal structure of Dronpa-Cu2+ · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5TLG6
Elsewhere: RCSB PDB 5HZT · PDBe 5HZT · UniProt Q5TLG6

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