MolNFT v1 · #40018 · protein
Crystal structure of the lingo-1 ectodomain
2ID5 · Leucine rich repeat neuronal 6A: “Crystal structure of the lingo-1 ectodomain”. X-ray diffraction, 2 ligands (NAG, MAN), 17 pockets (best druggability 0.74). MolNFT v1 #40018 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2ID5
- Type
- protein
- Length
- 1,886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine rich repeat neuronal 6A
- UniProt
- Q96FE5
- Ligands
- NAG, MAN
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine rich repeat neuronal 6A | protein | 470 | 6% helix, 27% strand | Q96FE5 |
| B | Leucine rich repeat neuronal 6A | protein | 473 | 6% helix, 27% strand | Q96FE5 |
| C | Leucine rich repeat neuronal 6A | protein | 472 | 6% helix, 27% strand | Q96FE5 |
| D | Leucine rich repeat neuronal 6A | protein | 471 | 6% helix, 27% strand | Q96FE5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.74 | 0.81 | 81 | empty |
| 2 | 605 | 0.73 | 0.81 | 73 | empty |
| 3 | 357 | 0.73 | 0.84 | 41 | empty |
| 4 | 266 | 0.68 | 0.84 | 38 | empty |
| 5 | 380 | 0.62 | 0.77 | 47 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1286 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1259 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1244 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1190 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 glycan, 20 disulfide (N-glycosylation, disulfide).
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 Q96FE5
- Elsewhere: RCSB PDB 2ID5 · PDBe 2ID5 · UniProt Q96FE5
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