MolNFT v1 · #26008 · protein
Fab fragment of plp-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-L-alanine
1WC7 · Fab fragment of catalytic antibody 15A9, light chain: “Fab fragment of plp-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-L-alanine”. X-ray diffraction, 2 ligands (PP3, IOD), 11 pockets (best druggability 0.67).…
- PDB
- 1WC7
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of catalytic antibody 15A9, light chain; Fab fragment of catalytic antibody…
- Ligands
- PP3, IOD
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab fragment of catalytic antibody 15A9, light chain | protein | 212 | 6% helix, 43% strand | — |
| B, H | Fab fragment of catalytic antibody 15A9, heavy chain | protein | 223 | 8% helix, 43% strand | — |
| L | Fab fragment of catalytic antibody 15A9, light chain | protein | 211 | 6% helix, 46% strand | — |
Ligands and binding sites
- PP3 · Alanyl-pyridoxal-5'-phosphate · ligand · chains A, B
- IOD · Iodide ion · ion · 5 copies · chains A, H, B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.67 | 0.75 | 87 | empty |
| 2 | 567 | 0.62 | 0.75 | 61 | empty |
| 3 | 581 | 0.62 | 0.74 | 50 | IOD |
| 4 | 89 | 0.42 | 0.79 | 19 | empty |
| 5 | 96 | 0.39 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1744 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1743 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 483 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1WC7 · Fab fragment of plp-dependent catalytic antibody 15A9 in complex with… · 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 1WC7 · PDBe 1WC7
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