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High resolution crystal structure of the discosoma red fluorescent protein (dsred)

Analyse High resolution crystal structure of the discosoma red fluorescent protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZGO
Type: protein
Length: 868 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Red fluorescent protein DRFP583
UniProt: Q9U6Y8
Ligands: CRQ
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Red fluorescent protein DRFP583	protein	217	6% helix, 57% strand	Q9U6Y8

Ligands and binding sites

CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.84	0.85	93	empty
2	86	0.75	0.97	30	CRQ
3	80	0.75	0.98	28	CRQ
4	79	0.72	0.96	27	CRQ
5	78	0.71	0.96	27	CRQ

Interfaces

6 interfaces between chains.

B–D · 1378 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1375 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1097 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1084 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 16 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

1ZGO · High Resolution Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed) · the same entry in another collection · chain A against A, TM-score 1.00
Q9U6Y8 · AlphaFold monomer V2.0 prediction for red fluorescent protein DRFP583 (Q9U6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9U6Y8
Elsewhere: RCSB PDB 1ZGO · PDBe 1ZGO · UniProt Q9U6Y8

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