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Deglycosylated nogo receptor with native disulfide structure 5

Analyse Deglycosylated nogo receptor with native disulfide structure 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O0O
Type: protein
Length: 2,507 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reticulon-4 receptor
UniProt: Q99PI8
Ligands: NAG, CL
Pockets: 16 · best druggability 0.75

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Reticulon-4 receptor	protein	316	12% helix, 15% strand	Q99PI8
B	Reticulon-4 receptor	protein	317	12% helix, 16% strand	Q99PI8
C	Reticulon-4 receptor	protein	313	12% helix, 16% strand	Q99PI8
D	Reticulon-4 receptor	protein	315	11% helix, 16% strand	Q99PI8
E	Reticulon-4 receptor	protein	315	12% helix, 15% strand	Q99PI8
F	Reticulon-4 receptor	protein	311	11% helix, 16% strand	Q99PI8
G	Reticulon-4 receptor	protein	312	11% helix, 15% strand	Q99PI8
H	Reticulon-4 receptor	protein	308	11% helix, 16% strand	Q99PI8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, H, B, E, D, C, G, F
CL · Chloride ion · ion · 94 copies · chains A, D, H, B, C, E, G, F
GOL · Glycerol · additive · 7 copies · chains A, D, H, B, F

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	785	0.75	0.79	76	CL
2	825	0.74	0.79	67	GOL, CL
3	750	0.74	0.79	71	CL
4	804	0.73	0.78	86	CL
5	743	0.73	0.79	80	CL

Interfaces

14 interfaces between chains.

A–H · 1144 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1104 Å² buried · 9 hydrogen bonds · protein-protein
B–H · 1097 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1096 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 1079 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 disulfide, 24 glycan (disulfide, N-glycosylation).

Compared structures

5O0O · Deglycosylated Nogo Receptor with native disulfide structure 5 · the same entry in another collection · chain H against H, TM-score 1.00
Q99PI8 · AlphaFold monomer V2.0 prediction for reticulon-4 receptor (Q99PI8) · a predicted model of the same protein · chain F against A, TM-score 0.94

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 Q99PI8
Elsewhere: RCSB PDB 5O0O · PDBe 5O0O · UniProt Q99PI8

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