MolNFT v1 · #156931 · protein
Catalytic domain of dbophma
6MJF: “Catalytic domain of dbophma”. X-ray diffraction, 1 ligand (SAH), 16 pockets (best druggability 0.86). MolNFT v1 #156931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MJF
- Type
- protein
- Length
- 2,221 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dbophm
- Ligands
- SAH
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dbophm | protein | 371 | 39% helix, 15% strand | — |
| B, D, F | Dbophm | protein | 370 | 38% helix, 15% strand | — |
| E | Dbophm | protein | 369 | 38% helix, 15% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.86 | 0.87 | 94 | empty |
| 2 | 1094 | 0.86 | 0.87 | 109 | SAH |
| 3 | 1186 | 0.85 | 0.86 | 109 | SAH |
| 4 | 1141 | 0.84 | 0.85 | 115 | SAH |
| 5 | 1174 | 0.84 | 0.84 | 109 | SAH |
Interfaces
5 interfaces between chains.
- C–D · 6116 Ų buried · 72 hydrogen bonds · protein-protein
- E–F · 6063 Ų buried · 72 hydrogen bonds · protein-protein
- A–B · 6050 Ų buried · 76 hydrogen bonds · protein-protein
- B–F · 380 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 89 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MJF · Catalytic Domain of dbOphMA · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6MJF · PDBe 6MJF
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