MolNFT v1 · #138013 · protein
Crystal structure of BAXP168G in complex with an activating antibody at high resolution
5W5Z · 3C10 Fab light chain: “Crystal structure of BAXP168G in complex with an activating antibody at high resolution”. X-ray diffraction, 4 pockets (best druggability 0.53). MolNFT v1 #138013 on GenesisL1: 3D structure, binding sites and…
- 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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