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The crystal structure of R43A mutant putative ryanodine receptor from bacteroides thetaiotaomicron vpi-5482

Analyse The crystal structure of R43A mutant putative ryanodine receptor from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N05
Type: protein
Length: 560 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ryanodine receptor
UniProt: Q8A5J2
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Putative ryanodine receptor	protein	93	48% helix, 11% strand	Q8A5J2
A, C, E	Putative ryanodine receptor	protein	94	48% helix, 11% strand	Q8A5J2
D	Putative ryanodine receptor	protein	93	48% helix, 11% strand	Q8A5J2
F	Putative ryanodine receptor	protein	92	51% helix, 10% strand	Q8A5J2

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains B, A, E, C

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	816	0.75	0.79	67	empty
2	839	0.75	0.79	60	empty
3	658	0.73	0.79	40	empty
4	195	0.50	0.77	30	empty
5	191	0.49	0.76	27	empty

Interfaces

6 interfaces between chains.

B–A · 2027 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2015 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1958 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 743 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 723 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

4N05 · The crystal structure of R43A mutant putative ryanodine receptor from Bacteroides… · 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 Q8A5J2
Elsewhere: RCSB PDB 4N05 · PDBe 4N05 · UniProt Q8A5J2

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