Research workbench
Crystal structure of BAXP168G in complex with an activating antibody at high resolution
Analyse Crystal structure of BAXP168G in complex with an activating antibody at high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W5Z
- Type
- protein
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C10 Fab light chain; 3C10 Fab heavy chain; Apoptosis regulator bax
- UniProt
- Q07812
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 3C10 Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| H | 3C10 Fab heavy chain | protein | 210 | 10% helix, 56% strand | — |
| A | Apoptosis regulator bax | protein | 109 | 57% helix, 0% strand | Q07812 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains L, H
- PG4 · Tetraethylene glycol · additive · 2 copies · chains L
- PGE · Triethylene glycol · additive · 2 copies · chains H, L
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.53 | 0.76 | 28 | empty |
| 2 | 345 | 0.53 | 0.73 | 46 | EDO, MES |
| 3 | 100 | 0.38 | 0.75 | 23 | empty |
| 4 | 64 | 0.30 | 0.74 | 13 | PGE |
Interfaces
3 interfaces between chains.
- L–H · 1571 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 397 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 280 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5W5Z · Crystal structure of BAXP168G in complex with an activating antibody at high resolution · the same entry in another collection · chain L against L, TM-score 1.00
- Q07812 · AlphaFold monomer V2.0 prediction for apoptosis regulator bax (Q07812) · a predicted model of the same protein · chain A against A, TM-score 0.80
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q07812
- Elsewhere: RCSB PDB 5W5Z · PDBe 5W5Z · UniProt Q07812
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