MolNFT v1 · #56175 · protein

Crystal structure of 22G, the wild-type protein of the photoswitchable GFP-like protein dronpa

2Z6X · Photochromic protein dronpa: “Crystal structure of 22G, the wild-type protein of the photoswitchable GFP-like protein dronpa”. X-ray diffraction, 1 ligand (GYC), 18 pockets (best druggability 0.85). MolNFT v1 #56175 on GenesisL1: 3D…

PDB: 2Z6X
Type: protein
Length: 1,717 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photochromic protein dronpa
Ligands: GYC
Pockets: 18 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Photochromic protein dronpa	protein	216	2% helix, 56% strand	—
B, E, F	Photochromic protein dronpa	protein	215	4% helix, 58% strand	—
C, D, G, H	Photochromic protein dronpa	protein	214	7% helix, 58% strand	—

Ligands and binding sites

GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	881	0.85	0.87	134	empty
2	1191	0.83	0.84	109	empty
3	83	0.77	0.99	27	GYC
4	82	0.76	0.98	25	GYC
5	79	0.76	0.99	26	GYC

Interfaces

11 interfaces between chains.

A–C · 1236 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1182 Å² buried · 21 hydrogen bonds · protein-protein
F–H · 1138 Å² buried · 24 hydrogen bonds · protein-protein
E–G · 1123 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 913 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 covalent (covalent ligand).

Compared structures

2Z6X · Crystal structure of 22G, the wild-type protein of the photoswitchable GFP-like protein… · 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
Elsewhere: RCSB PDB 2Z6X · PDBe 2Z6X

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