MolNFT v1 · #101177 · protein
Crystal structure of Fab 8B10 in complex with mpts
4NJ9 · 8B10 light chain: “Crystal structure of Fab 8B10 in complex with mpts”. X-ray diffraction, 2 ligands (2M9, ZN), 3 pockets (best druggability 0.59). MolNFT v1 #101177 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NJ9
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8B10 light chain; 8B10 heavy chain
- UniProt
- Q52L95, Q9D8L4
- Ligands
- 2M9, ZN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 8B10 light chain | protein | 212 | 5% helix, 53% strand | Q52L95 |
| H | 8B10 heavy chain | protein | 217 | 8% helix, 52% strand | Q9D8L4 |
Ligands and binding sites
- 2M9 · 8-methoxypyrene-1,3,6-trisulfonic acid · ligand · chains L, H
- ZN · Zinc ion · metal · 6 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.59 | 0.74 | 47 | empty |
| 2 | 140 | 0.41 | 0.74 | 26 | empty |
| 3 | 70 | 0.33 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 1910 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4NJ9 · Crystal structure of Fab 8B10 in complex with MPTS · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q52L95
- Every structure of UniProt Q9D8L4
- Elsewhere: RCSB PDB 4NJ9 · PDBe 4NJ9 · UniProt Q52L95 · UniProt Q9D8L4
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