MolNFT v1 · #116963 · protein

Crystal structure of rsfolder in the fluorescent on-state

5DTZ · Green fluorescent protein: “Crystal structure of rsfolder in the fluorescent on-state”. X-ray diffraction, 1 ligand (PIA), 9 pockets (best druggability 0.76). MolNFT v1 #116963 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5DTZ
Type: protein
Length: 918 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: PIA
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	230	10% helix, 51% strand	P42212
B, D	Green fluorescent protein	protein	229	11% helix, 51% strand	P42212
C	Green fluorescent protein	protein	230	12% helix, 51% strand	P42212

Ligands and binding sites

PIA · [(4Z)-2-[(1S)-1-aminoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, D

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.76	0.98	25	PIA
2	76	0.74	0.97	23	PIA
3	70	0.74	0.98	21	PIA
4	59	0.72	0.98	19	PIA
5	504	0.70	0.80	61	empty

Interfaces

4 interfaces between chains.

A–C · 549 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 308 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 299 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 288 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

5DTZ · Crystal structure of rsFolder in the fluorescent on-state · the same entry in another collection · chain D against D, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B 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 5DTZ · PDBe 5DTZ · UniProt P42212

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