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Crystal structure of pslssmkate, a photoswitchable lssmkate variant

Analyse Crystal structure of pslssmkate, a photoswitchable lssmkate variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NWS
Type: protein
Length: 446 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein
Ligands: NRQ
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Fluorescent protein	protein	223	6% helix, 57% strand	—

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 · 2 copies · chains A, B

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

Pockets

5 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	94	0.77	0.98	26	NRQ
2	86	0.75	0.98	27	NRQ
3	75	0.31	0.74	25	empty
4	51	0.30	0.76	14	empty
5	64	0.29	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 1563 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

4NWS · Crystal structure of PSLssmKate, a photoswitchable LSSmKate variant · the same entry in another collection · chain B against B, 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 4NWS · PDBe 4NWS

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