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Closed dimer of Y77A mutant putative ryanodine receptor from bacteroides thetaiotaomicron vpi-5482

Analyse Closed dimer of Y77A mutant putative ryanodine receptor from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UG5
Type: protein
Length: 561 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ryanodine receptor
UniProt: Q8A5J2
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, I	Putative ryanodine receptor	protein	93	48% helix, 11% strand	Q8A5J2
E, G	Putative ryanodine receptor	protein	95	46% helix, 11% strand	Q8A5J2
K	Putative ryanodine receptor	protein	92	49% helix, 11% strand	Q8A5J2

Ligands and binding sites

GOL · Glycerol · additive · 8 copies · chains A, C, E, G, I, K

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

Pockets

5 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	813	0.73	0.78	53	empty
2	789	0.72	0.78	61	empty
3	735	0.69	0.76	53	empty
4	179	0.49	0.77	30	empty
5	121	0.46	0.78	19	empty

Interfaces

5 interfaces between chains.

G–K · 2012 Å² buried · 19 hydrogen bonds · protein-protein
E–I · 1999 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1951 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 732 Å² buried · 19 hydrogen bonds · protein-protein
C–G · 724 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

6UG5 · Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron… · 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
Every structure of UniProt Q8A5J2
Elsewhere: RCSB PDB 6UG5 · PDBe 6UG5 · UniProt Q8A5J2

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