MolNFT v1 · #61265 · protein
Crystal structure of FABOX108
3DGG · FABOX108 light chain fragment: “Crystal structure of FABOX108”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.62). MolNFT v1 #61265 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DGG
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FABOX108 light chain fragment; FABOX108 heavy chain fragment
- Ligands
- MG
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FABOX108 light chain fragment | protein | 217 | 6% helix, 50% strand | — |
| B | FABOX108 heavy chain fragment | protein | 212 | 8% helix, 52% strand | — |
| C | FABOX108 light chain fragment | protein | 215 | 7% helix, 51% strand | — |
| D | FABOX108 heavy chain fragment | protein | 215 | 7% helix, 53% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.62 | 0.75 | 66 | empty |
| 2 | 359 | 0.55 | 0.75 | 47 | empty |
| 3 | 75 | 0.49 | 0.84 | 26 | empty |
| 4 | 89 | 0.46 | 0.80 | 18 | empty |
| 5 | 118 | 0.38 | 0.74 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1797 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1763 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3DGG · Crystal structure of FabOX108 · 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 3DGG · PDBe 3DGG
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