Research workbench
Crystal structure of a calcium- and sodium-bound mouse olfactomedin-1 disulfide-linked dimer of the olfactomedin domain and part of coiled coil
Analyse Crystal structure of a calcium- and sodium-bound mouse olfactomedin-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QM3
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Noelin
- UniProt
- O88998
- Ligands
- NAG, CA, NA
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Noelin | protein | 268 | 9% helix, 49% strand | O88998 |
| B | Noelin | protein | 266 | 8% helix, 48% strand | O88998 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- CAC · Cacodylate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.44 | 0.76 | 28 | empty |
| 2 | 71 | 0.41 | 0.80 | 16 | empty |
| 3 | 134 | 0.38 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 464 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6QM3 · Crystal structure of a calcium- and sodium-bound mouse Olfactomedin-1 disulfide-linked… · 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 B 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 6QM3 · PDBe 6QM3 · UniProt O88998
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