MolNFT v1 · #99526 · protein
Crystal structure of unliganded anti-DNA Fab A52
4M61 · Fab A52 light chain: “Crystal structure of unliganded anti-DNA Fab A52”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.65). MolNFT v1 #99526 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4M61
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab A52 light chain; Fab A52 heavy chain
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab A52 light chain | protein | 219 | 6% helix, 53% strand | — |
| B, D | Fab A52 heavy chain | protein | 220 | 7% helix, 54% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.65 | 0.75 | 58 | empty |
| 2 | 449 | 0.58 | 0.74 | 57 | SO4 |
| 3 | 126 | 0.45 | 0.77 | 26 | empty |
| 4 | 139 | 0.44 | 0.76 | 20 | empty |
| 5 | 84 | 0.33 | 0.74 | 18 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1870 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1838 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 369 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4M61 · Crystal structure of unliganded anti-DNA Fab A52 · 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 4M61 · PDBe 4M61
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.