MolNFT v1 · #71431 · protein

Crystal structure of mouse rank

3ME4 · Tumor necrosis factor receptor superfamily member 11A: “Crystal structure of mouse rank”. X-ray diffraction, 3 ligands (NA, CL, SO4), 4 pockets (best druggability 0.58). MolNFT v1 #71431 on GenesisL1: 3D structure, binding sites and…

PDB: 3ME4
Type: protein
Length: 319 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor necrosis factor receptor superfamily member 11A
UniProt: O35305
Ligands: NA, CL, SO4
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor necrosis factor receptor superfamily member 11A	protein	169	4% helix, 36% strand	O35305
B	Tumor necrosis factor receptor superfamily member 11A	protein	150	2% helix, 35% strand	O35305

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 4 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A

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	226	0.58	0.80	54	GOL
2	269	0.57	0.78	29	empty
3	71	0.36	0.77	20	CL
4	96	0.34	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 1287 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

3ME4 · Crystal structure of mouse RANK · the same entry in another collection · chain A against A, TM-score 1.00
O35305 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain B against A, TM-score 0.75

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 O35305
Elsewhere: RCSB PDB 3ME4 · PDBe 3ME4 · UniProt O35305

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