MolNFT v1 · #6405 · protein
Assembly domain of cartilage oligomeric matrix protein in complex with all-trans retinol
1FBM · Protein (cartilage oligomeric matrix protein): “Assembly domain of cartilage oligomeric matrix protein in complex with all-trans retinol”. X-ray diffraction, 1 ligand (RTL), 3 pockets (best druggability 0.82). MolNFT v1 #6405 on…
- PDB
- 1FBM
- Type
- protein
- Length
- 230 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cartilage oligomeric matrix protein)
- UniProt
- P35444
- Ligands
- RTL
- 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 | Protein (cartilage oligomeric matrix protein) | protein | 46 | 80% helix, 0% strand | P35444 |
Ligands and binding sites
- RTL · Retinol · ligand · 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 | 204 | 0.82 | 0.95 | 34 | RTL |
| 2 | 244 | 0.81 | 0.93 | 39 | empty |
| 3 | 291 | 0.63 | 0.79 | 24 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1223 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1173 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1153 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1132 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1107 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1FBM · Assembly domain of cartilage oligomeric matrix protein in complex with all-trans retinol · 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 0.79
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 1FBM · PDBe 1FBM · UniProt P35444
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