Research workbench
The crystal structure of the signature domain of cartilage oligomeric matrix protein.
Analyse The crystal structure of the signature domain of cartilage oligomeric matrix… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FBY
- Type
- protein
- Length
- 1,605 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cartilage oligomeric matrix protein
- UniProt
- P49747
- Ligands
- NAG, MAN, CA, SO4
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cartilage oligomeric matrix protein | protein | 535 | 8% helix, 23% strand | P49747 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, C
- CA · Calcium ion · metal · 88 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.70 | 0.76 | 86 | SO4 |
| 2 | 677 | 0.67 | 0.76 | 67 | empty |
| 3 | 758 | 0.67 | 0.75 | 74 | SO4 |
| 4 | 419 | 0.58 | 0.75 | 45 | empty |
| 5 | 350 | 0.56 | 0.75 | 38 | CA |
Interfaces
3 interfaces between chains.
- A–C · 648 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 459 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 403 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3FBY · The crystal structure of the signature domain of cartilage oligomeric matrix protein. · the same entry in another collection · chain A against A, TM-score 1.00
- P49747 · AlphaFold monomer V2.0 prediction for cartilage oligomeric matrix protein (P49747) · a predicted model of the same protein · chain C 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 P49747
- Elsewhere: RCSB PDB 3FBY · PDBe 3FBY · UniProt P49747
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