MolNFT v1 · #117117 · protein
FAB43.1 complex with flourescein
5DYO · Fab 43.1 heavy chain: “FAB43.1 complex with flourescein”. X-ray diffraction, 2 ligands (FLU, SO4), 8 pockets (best druggability 0.64). MolNFT v1 #117117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DYO
- Type
- protein
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 43.1 heavy chain; Fab 43.1 light chain
- Ligands
- FLU, SO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 43.1 heavy chain | protein | 205 | 6% helix, 50% strand | — |
| B | Fab 43.1 light chain | protein | 218 | 6% helix, 52% strand | — |
| H | Fab 43.1 heavy chain | protein | 212 | 10% helix, 49% strand | — |
| L | Fab 43.1 light chain | protein | 216 | 6% helix, 51% strand | — |
Ligands and binding sites
- FLU · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid · ligand · 2 copies · chains A, B, L, H
- SO4 · Sulfate ion · ion · 5 copies · chains B, L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.64 | 0.74 | 58 | empty |
| 2 | 535 | 0.61 | 0.75 | 62 | empty |
| 3 | 239 | 0.58 | 0.79 | 43 | SO4 |
| 4 | 98 | 0.57 | 0.86 | 14 | FLU |
| 5 | 112 | 0.56 | 0.84 | 17 | FLU |
Interfaces
5 interfaces between chains.
- H–L · 1776 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1707 Ų buried · 18 hydrogen bonds · protein-protein
- B–H · 244 Ų buried · 3 hydrogen bonds · protein-protein
- A–L · 224 Ų buried · 2 hydrogen bonds · protein-protein
- B–L · 203 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5DYO · Fab43.1 complex with flourescein · 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 5DYO · PDBe 5DYO
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