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Crystal structure of circular permutated red fluorescent protein MKATE(CP 154-153)

Analyse Crystal structure of circular permutated red fluorescent protein MKATE(CP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RWT
Type: protein
Length: 1,872 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fluorescent protein FP480,FLUORESCENT protein FP480
UniProt: D0VX33
Ligands: NRQ, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, A, B, C, D, E, G, H	Fluorescent protein FP480,FLUORESCENT protein FP480	protein	234	9% helix, 53% strand	D0VX33

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 · 8 copies · chains F, A, B, C, D, E, G, H
MG · Magnesium ion · metal · chains A, G

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.85	0.91	50	empty
2	567	0.84	0.90	53	empty
3	116	0.79	0.98	28	NRQ
4	115	0.78	0.97	27	NRQ
5	97	0.76	0.97	27	NRQ

Interfaces

13 interfaces between chains.

D–H · 1640 Å² buried · 23 hydrogen bonds · protein-protein
C–E · 1632 Å² buried · 26 hydrogen bonds · protein-protein
F–B · 1621 Å² buried · 26 hydrogen bonds · protein-protein
A–G · 1611 Å² buried · 22 hydrogen bonds · protein-protein
F–A · 969 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 cofactor (chromophore).

Compared structures

3RWT · Crystal structure of circular permutated Red Fluorescent Protein mKate(cp 154-153) · the same entry in another collection · chain F against F, 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
Every structure of UniProt D0VX33
Elsewhere: RCSB PDB 3RWT · PDBe 3RWT · UniProt D0VX33

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