MolNFT v1 · #30788 · protein
A mutation designed to alter crystal packing permits structural analysis of a tight-binding fluorescein-scfv complex
2A9N · Fluorescein-scfv light chain: “A mutation designed to alter crystal packing permits structural analysis of a tight-binding fluorescein-scfv…”. X-ray diffraction, 1 ligand (ORE), 6 pockets (best druggability 0.61). MolNFT v1 #30788…
- PDB
- 2A9N
- Type
- protein
- Length
- 470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescein-scfv light chain; Fluorescein-scfv heavy chain
- Ligands
- ORE
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fluorescein-scfv light chain | protein | 109 | 5% helix, 50% strand | — |
| H, I | Fluorescein-scfv heavy chain | protein | 126 | 7% helix, 48% strand | — |
| M | Fluorescein-scfv light chain | protein | 109 | 5% helix, 50% strand | — |
Ligands and binding sites
- ORE · 4-(2,7-difluoro-6-hydroxy-3-oxo-3H-xanthen-9-yl)isophthalic acid · ligand · 2 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.61 | 0.75 | 54 | empty |
| 2 | 170 | 0.59 | 0.82 | 23 | ORE |
| 3 | 168 | 0.57 | 0.81 | 24 | ORE |
| 4 | 268 | 0.53 | 0.76 | 55 | empty |
| 5 | 51 | 0.31 | 0.77 | 13 | empty |
Interfaces
5 interfaces between chains.
- M–I · 912 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 885 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 564 Ų buried · 2 hydrogen bonds · protein-protein
- L–I · 25 Ų buried · 0 hydrogen bonds · protein-protein
- H–M · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2A9N · PDBe 2A9N
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