MolNFT v1 · #62110 · protein

Crystal structure analysis of FP611

3E5W · Red fluorescent protein EQFP611: “Crystal structure analysis of FP611”. X-ray diffraction, 1 ligand (NRQ), 10 pockets (best druggability 0.87). MolNFT v1 #62110 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3E5W
Type: protein
Length: 904 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Red fluorescent protein EQFP611
UniProt: Q8ISF8
Ligands: NRQ
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Red fluorescent protein EQFP611	protein	226	4% helix, 55% strand	Q8ISF8

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

10 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	851	0.87	0.89	80	empty
2	83	0.77	0.99	26	NRQ
3	86	0.77	0.99	24	NRQ
4	85	0.76	0.98	28	NRQ
5	88	0.75	0.97	27	NRQ

Interfaces

6 interfaces between chains.

A–D · 1843 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 1833 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1046 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1035 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 59 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

3E5W · Crystal Structure Analysis of FP611 · the same entry in another collection · chain A against A, TM-score 1.00
Q8ISF8 · AlphaFold monomer V2.0 prediction for red fluorescent protein EQFP611 (Q8ISF8) · 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 Q8ISF8
Elsewhere: RCSB PDB 3E5W · PDBe 3E5W · UniProt Q8ISF8

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