MolNFT v1 · #102635 · protein

Blue fluorescent protein MKALAMA1

4ORN: “Blue fluorescent protein MKALAMA1”. X-ray diffraction, 3 ligands (GYS, SO4, CL), 4 pockets (best druggability 0.72). MolNFT v1 #102635 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4ORN
Type: protein
Length: 456 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MKALAMA1
UniProt: P42212
Ligands: GYS, SO4, CL
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	MKALAMA1	protein	228	11% helix, 50% strand	P42212

Ligands and binding sites

GYS · [(4Z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.72	0.97	24	GYS
2	68	0.71	0.96	23	GYS
3	367	0.61	0.77	42	SO4
4	151	0.43	0.75	30	SO4

Interfaces

1 interface between chains.

A–B · 778 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor, 2 modified (chromophore, oxidation).

Compared structures

4ORN · Blue Fluorescent Protein mKalama1 · the same entry in another collection · chain A against A, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · 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 P42212
Elsewhere: RCSB PDB 4ORN · PDBe 4ORN · UniProt P42212

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