MolNFT v1 · #190772 · protein

Sandercyanin fluorescent protein - Y142A variant bound to bv

7YX1: “Sandercyanin fluorescent protein - Y142A variant bound to bv”. X-ray diffraction, 1 ligand (BLA), 5 pockets (best druggability 0.75). MolNFT v1 #190772 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7YX1
Type: protein
Length: 338 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sandercyanin fluorescent protein
UniProt: A0A1D5B367
Ligands: BLA
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sandercyanin fluorescent protein	protein	169	9% helix, 43% strand	A0A1D5B367

Ligands and binding sites

BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	411	0.75	0.84	44	BLA
2	451	0.73	0.83	54	BLA
3	147	0.46	0.77	29	empty
4	153	0.45	0.76	29	empty
5	62	0.39	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 670 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7YX1 · Sandercyanin fluorescent protein - Y142A variant bound to BV · 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 A0A1D5B367
Elsewhere: RCSB PDB 7YX1 · PDBe 7YX1 · UniProt A0A1D5B367

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