MolNFT v1 · #32314 · protein
Fab fragment of plp-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine
2BMK · Fab fragment of catalytic antibody 15A9, light chain: “Fab fragment of plp-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine”. X-ray diffraction, 2 ligands (PDD, IOD), 10 pockets (best druggability 0.69).…
- PDB
- 2BMK
- Type
- protein
- Length
- 870 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
- PDD, IOD
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Fab fragment of catalytic antibody 15A9, light chain | protein | 213 | 6% helix, 52% strand | — |
| B | Fab fragment of catalytic antibody 15A9, heavy chain | protein | 223 | 8% helix, 51% strand | — |
| H | Fab fragment of catalytic antibody 15A9, heavy chain | protein | 221 | 8% helix, 49% strand | — |
Ligands and binding sites
- PDD · N-(5'-phosphopyridoxyl)-D-alanine · ligand · 2 copies · chains A, B, H, L
- IOD · Iodide ion · ion · 6 copies · chains B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.69 | 0.76 | 70 | empty |
| 2 | 567 | 0.63 | 0.75 | 61 | empty |
| 3 | 540 | 0.62 | 0.75 | 59 | empty |
| 4 | 185 | 0.48 | 0.76 | 35 | empty |
| 5 | 156 | 0.44 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1767 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1725 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 525 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2BMK · Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with… · the same entry in another collection · chain B against B, 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 2BMK · PDBe 2BMK
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