MolNFT v1 · #141480 · protein

Crystal structure of human LRRTM2

5Z8X · Leucine-rich repeat transmembrane neuronal protein 2: “Crystal structure of human LRRTM2”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.74). MolNFT v1 #141480 on GenesisL1: 3D structure, binding sites and…

PDB: 5Z8X
Type: protein
Length: 1,312 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leucine-rich repeat transmembrane neuronal protein 2
UniProt: O43300
Ligands: NAG
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Leucine-rich repeat transmembrane neuronal protein 2	protein	328	8% helix, 16% strand	O43300

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	498	0.74	0.83	59	empty
2	201	0.50	0.76	26	empty
3	112	0.43	0.77	20	empty

Interfaces

4 interfaces between chains.

A–C · 792 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 790 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 685 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 193 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5Z8X · Crystal structure of human LRRTM2 · the same entry in another collection · chain A against A, TM-score 1.00
O43300 · AlphaFold monomer V2.0 prediction for leucine-rich repeat transmembrane neuronal protein… · 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 O43300
Elsewhere: RCSB PDB 5Z8X · PDBe 5Z8X · UniProt O43300

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