MolNFT v1 · #94660 · protein

Crystal structure of fluorescent protein unag wild type

4I3B · Bilirubin-inducible fluorescent protein unag: “Crystal structure of fluorescent protein unag wild type”. X-ray diffraction, 1 ligand (BLR), 8 pockets (best druggability 0.89). MolNFT v1 #94660 on GenesisL1: 3D structure, binding…

PDB: 4I3B
Type: protein
Length: 829 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bilirubin-inducible fluorescent protein unag
UniProt: P0DM59
Ligands: BLR
Pockets: 8 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 14% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Bilirubin-inducible fluorescent protein unag	protein	139	14% helix, 54% strand	P0DM59
B, C, D	Bilirubin-inducible fluorescent protein unag	protein	138	14% helix, 55% strand	P0DM59
F	Bilirubin-inducible fluorescent protein unag	protein	137	14% helix, 55% strand	P0DM59

Ligands and binding sites

BLR · 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · 6 copies · chains A, B, C, D, E, F
PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, D, C, E, F

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

Pockets

8 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	1096	0.89	0.91	100	BLR, PEG
2	1161	0.89	0.91	111	BLR, PEG
3	1161	0.89	0.90	109	BLR, PEG
4	314	0.63	0.80	38	empty
5	260	0.54	0.76	35	PEG

Interfaces

8 interfaces between chains.

B–D · 600 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 584 Å² buried · 2 hydrogen bonds · protein-protein
C–E · 556 Å² buried · 3 hydrogen bonds · protein-protein
B–E · 428 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 327 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4I3B · Crystal structure of fluorescent protein UnaG wild type · the same entry in another collection · chain E against E, TM-score 1.00
P0DM59 · AlphaFold monomer V2.0 prediction for bilirubin-inducible fluorescent protein unag… · a predicted model of the same protein · chain F against A, TM-score 0.94

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 P0DM59
Elsewhere: RCSB PDB 4I3B · PDBe 4I3B · UniProt P0DM59

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