MolNFT v1 · #102347 · protein

Mcardinal V218E

4OJ0 · Fluorescent protein FP480: “Mcardinal V218E”. X-ray diffraction, 1 ligand (NRQ), 7 pockets (best druggability 0.77). MolNFT v1 #102347 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4OJ0
Type: protein
Length: 896 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein FP480
UniProt: D0VX33
Ligands: NRQ
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Fluorescent protein FP480	protein	224	6% helix, 56% strand	D0VX33

Ligands and binding sites

NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-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

7 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	1156	0.77	0.79	121	empty
2	95	0.77	0.98	26	NRQ
3	93	0.76	0.98	26	NRQ
4	94	0.76	0.98	28	NRQ
5	99	0.76	0.97	27	NRQ

Interfaces

6 interfaces between chains.

A–D · 1595 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 385 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 248 Å² buried · 1 hydrogen bond · protein-protein
A–C · 188 Å² buried · 1 hydrogen bond · protein-protein
A–B · 87 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4OJ0 · mCardinal V218E · 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 D0VX33
Elsewhere: RCSB PDB 4OJ0 · PDBe 4OJ0 · UniProt D0VX33

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