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Bax domain swapped dimer induced by octylmaltoside

Analyse Bax domain swapped dimer induced by octylmaltoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BD7
Type: protein
Length: 560 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptosis regulator bax
UniProt: Q07812
Ligands: PR, CL
Pockets: 7 · best druggability 0.50

Structure

x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apoptosis regulator bax	protein	144	74% helix, 0% strand	Q07812
B	Apoptosis regulator bax	protein	152	70% helix, 0% strand	Q07812
C	Apoptosis regulator bax	protein	132	76% helix, 0% strand	Q07812
D	Apoptosis regulator bax	protein	132	74% helix, 0% strand	Q07812

Ligands and binding sites

PR · Praseodymium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.50	0.80	29	empty
2	69	0.49	0.84	18	empty
3	130	0.48	0.78	26	empty
4	114	0.43	0.77	23	empty
5	122	0.38	0.73	33	empty

Interfaces

5 interfaces between chains.

A–B · 4111 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 3425 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 210 Å² buried · 1 hydrogen bond · protein-protein
A–D · 129 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 67 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4BD7 · Bax domain swapped dimer induced by octylmaltoside · the same entry in another collection · chain D against D, 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 0.62

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 4BD7 · PDBe 4BD7 · UniProt Q07812

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