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Mouse rankl structure at 1.9A resolution

Analyse Mouse rankl structure at 1.9A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1S55
Type: protein
Length: 468 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor ligand superfamily member 11
UniProt: O35235
Ligands: CL
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Tumor necrosis factor ligand superfamily member 11	protein	156	4% helix, 57% strand	O35235

Ligands and binding sites

CL · Chloride ion · ion · 3 copies · chains A, C, B

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

Pockets

4 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	52	0.72	0.99	12	empty
2	316	0.65	0.81	38	empty
3	62	0.38	0.79	14	empty
4	53	0.28	0.75	20	CL

Interfaces

3 interfaces between chains.

A–C · 1104 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1080 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1051 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

1S55 · Mouse RANKL Structure at 1.9A Resolution · the same entry in another collection · chain C against C, TM-score 1.00
O35235 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 11… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O35235
Elsewhere: RCSB PDB 1S55 · PDBe 1S55 · UniProt O35235

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