MolNFT v1 · #63511 · protein
The crystal structure of the signature domain of cartilage oligomeric matrix protein.
3FBY: “The crystal structure of the signature domain of cartilage oligomeric matrix protein.”. X-ray diffraction, 4 ligands (NAG, MAN, CA), 14 pockets (best druggability 0.70). MolNFT v1 #63511 on GenesisL1: 3D structure, binding sites and…
- 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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