MolNFT v1 · #38402 · protein

Crystal structure of stony coral fluorescent protein kaede, green form

2GW3: “Crystal structure of stony coral fluorescent protein kaede, green form”. X-ray diffraction, 2 ligands (CR8, NI), 3 pockets (best druggability 0.74). MolNFT v1 #38402 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GW3
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kaede
Ligands: CR8, NI
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Kaede	protein	218	3% helix, 57% strand	—

Ligands and binding sites

CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 4 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	70	0.74	0.98	25	CR8
2	73	0.71	0.96	27	CR8
3	138	0.45	0.77	25	empty

Interfaces

1 interface between chains.

A–B · 1093 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

2GW3 · Crystal structure of stony coral fluorescent protein Kaede, green form · 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
Elsewhere: RCSB PDB 2GW3 · PDBe 2GW3

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