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HROBO2 ectodomain

Analyse HROBO2 ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IAA
Type: protein
Length: 2,445 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Roundabout homolog 2
UniProt: Q9HCK4
Ligands: NAG, MAN, BMA
Pockets: 19 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Roundabout homolog 2	protein	815	3% helix, 44% strand	Q9HCK4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C
BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C

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

Pockets

19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.79	0.81	101	empty
2	1178	0.75	0.78	93	empty
3	286	0.60	0.79	34	empty
4	319	0.60	0.78	39	empty
5	263	0.58	0.78	34	empty

Interfaces

2 interfaces between chains.

B–C · 712 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 402 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 33 modified, 15 disulfide, 6 glycan (engineered, disulfide, N-glycosylation).

Compared structures

6IAA · hRobo2 ectodomain · the same entry in another collection · chain A against A, TM-score 1.00
Q9HCK4 · AlphaFold monomer V2.0 prediction for roundabout homolog 2 (Q9HCK4) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9HCK4
Elsewhere: RCSB PDB 6IAA · PDBe 6IAA · UniProt Q9HCK4

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