MolNFT v1 · #140905 · protein
Crystal structure of human osteomodulin
5YQ5: “Crystal structure of human osteomodulin”. X-ray diffraction, 2 ligands (NAG, PO4), 7 pockets (best druggability 0.76). MolNFT v1 #140905 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YQ5
- Type
- protein
- Length
- 1,217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osteomodulin
- UniProt
- Q99983
- Ligands
- NAG, PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Osteomodulin | protein | 302 | 8% helix, 15% strand | Q99983 |
| B | Osteomodulin | protein | 306 | 8% helix, 14% strand | Q99983 |
| C | Osteomodulin | protein | 304 | 8% helix, 14% strand | Q99983 |
| D | Osteomodulin | protein | 305 | 8% helix, 14% strand | Q99983 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.76 | 0.78 | 115 | PO4 |
| 2 | 561 | 0.72 | 0.80 | 61 | empty |
| 3 | 96 | 0.48 | 0.81 | 23 | empty |
| 4 | 58 | 0.36 | 0.78 | 13 | empty |
| 5 | 61 | 0.35 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–D · 739 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 638 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 631 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 451 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 13 glycan (disulfide, N-glycosylation).
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 Q99983
- Elsewhere: RCSB PDB 5YQ5 · PDBe 5YQ5 · UniProt Q99983
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