MolNFT v1 · #113682 · protein
Structure of a mouse olfactomedin-1 disulfide-linked dimer of the olfactomedin domain and part of the coiled coil
5AMO · Noelin: “Structure of a mouse olfactomedin-1 disulfide-linked dimer of the olfactomedin domain and part of the coiled…”. X-ray diffraction, 2 ligands (NAG, CL), 6 pockets (best druggability 0.54). MolNFT v1 #113682 on GenesisL1: 3D…
- PDB
- 5AMO
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Noelin
- UniProt
- O88998
- Ligands
- NAG, CL
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Noelin | protein | 253 | 8% helix, 47% strand | O88998 |
| B | Noelin | protein | 257 | 8% helix, 49% strand | O88998 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.54 | 0.74 | 41 | CL |
| 2 | 120 | 0.46 | 0.78 | 25 | empty |
| 3 | 87 | 0.41 | 0.78 | 19 | empty |
| 4 | 70 | 0.41 | 0.80 | 21 | empty |
| 5 | 67 | 0.36 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 492 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 5AMO · Structure of a mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and… · the same entry in another collection · chain A against A, TM-score 1.00
- O88998 · AlphaFold monomer V2.0 prediction for noelin (O88998) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 O88998
- Elsewhere: RCSB PDB 5AMO · PDBe 5AMO · UniProt O88998
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