Research workbench
Third lrr domain of human SLIT2
Analyse Third 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
- 2V70
- Type
- protein
- Length
- 840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Slit homolog 2 protein N-product
- UniProt
- O94813
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Slit homolog 2 protein N-product | protein | 210 | 13% helix, 19% strand | O94813 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.52 | 0.78 | 29 | empty |
| 2 | 140 | 0.44 | 0.77 | 24 | empty |
| 3 | 64 | 0.39 | 0.80 | 14 | empty |
| 4 | 141 | 0.38 | 0.73 | 21 | empty |
| 5 | 72 | 0.37 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 483 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 2V70 · PDBe 2V70 · UniProt O94813
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