Research workbench

Second lrr domain of human SLIT2

Analyse Second lrr domain of human SLIT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V9S
Type: protein
Length: 828 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Slit homolog 2 protein N-product
UniProt: O94813
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Slit homolog 2 protein N-product	protein	207	6% helix, 17% strand	O94813

Ligands and binding sites

GOL · Glycerol · additive · chains B
PEG · Di(hydroxyethyl)ether · additive · chains D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	569	0.65	0.76	55	empty
2	554	0.64	0.76	54	PEG
3	352	0.54	0.74	49	empty
4	164	0.44	0.75	21	empty
5	93	0.36	0.76	15	empty

Interfaces

4 interfaces between chains.

B–C · 785 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 784 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 454 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 427 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 modified (disulfide, oxidation).

Compared structures

2V9S · Second LRR domain of human Slit2 · the same entry in another collection · chain A against A, TM-score 1.00
O94813 · AlphaFold monomer V2.0 prediction for slit homolog 2 protein (O94813) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O94813
Elsewhere: RCSB PDB 2V9S · PDBe 2V9S · UniProt O94813

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