MolNFT v1 · #25025 · protein
Assembly domain of cartilage oligomeric matrix protein
1VDF: “Assembly domain of cartilage oligomeric matrix protein”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.82). MolNFT v1 #25025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VDF
- Type
- protein
- Length
- 230 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cartilage oligomeric matrix protein
- UniProt
- P35444
- Ligands
- CL
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cartilage oligomeric matrix protein | protein | 46 | 80% helix, 0% strand | P35444 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.82 | 0.93 | 37 | empty |
| 2 | 155 | 0.81 | 0.96 | 37 | CL |
| 3 | 178 | 0.56 | 0.80 | 20 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1200 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1193 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1127 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1124 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1122 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1VDF · Assembly domain of cartilage oligomeric matrix protein · the same entry in another collection · chain E against E, TM-score 1.00
- P35444 · AlphaFold monomer V2.0 prediction for cartilage oligomeric matrix protein (P35444) · a predicted model of the same protein · chain E against A, TM-score 0.78
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 P35444
- Elsewhere: RCSB PDB 1VDF · PDBe 1VDF · UniProt P35444
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