MolNFT v1 · #102610 · protein

Crystal structure of mcardinal far-red fluorescent protein

4OQW · Fluorescent protein FP480: “Crystal structure of mcardinal far-red fluorescent protein”. X-ray diffraction, 1 ligand (NRQ), 20 pockets (best druggability 0.86). MolNFT v1 #102610 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4OQW
Type: protein
Length: 1,728 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein FP480
UniProt: D0VX33
Ligands: NRQ
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fluorescent protein FP480	protein	225	8% helix, 56% strand	D0VX33
B	Fluorescent protein FP480	protein	223	4% helix, 57% strand	D0VX33
C	Fluorescent protein FP480	protein	222	5% helix, 57% strand	D0VX33
D	Fluorescent protein FP480	protein	225	3% helix, 55% strand	D0VX33
E	Fluorescent protein FP480	protein	213	3% helix, 57% strand	D0VX33
F	Fluorescent protein FP480	protein	214	3% helix, 54% strand	D0VX33
G	Fluorescent protein FP480	protein	211	6% helix, 49% strand	D0VX33
H	Fluorescent protein FP480	protein	195	3% helix, 46% 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 · 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

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.86	0.92	58	empty
2	178	0.81	0.97	33	NRQ
3	390	0.78	0.88	41	NRQ
4	133	0.78	0.96	31	NRQ
5	108	0.77	0.97	31	NRQ

Interfaces

12 interfaces between chains.

A–C · 1534 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1344 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1006 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1004 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 912 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 cofactor, 16 modified (chromophore, methylation).

Compared structures

4OQW · Crystal structure of mCardinal far-red fluorescent 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
Every structure of UniProt D0VX33
Elsewhere: RCSB PDB 4OQW · PDBe 4OQW · UniProt D0VX33

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