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Crystal structure of human soul BH3 domain in complex with BCL-xl

Analyse Crystal structure of human soul BH3 domain in complex with BCL-xl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R85
Type: protein
Length: 633 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1; Heme-binding protein 2
UniProt: Q07817, Q9Y5Z4
Ligands: SO4
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 6 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	BCL-2-like protein 1	protein	138	78% helix, 0% strand	Q07817
C, D	BCL-2-like protein 1	protein	139	78% helix, 0% strand	Q07817
E	Heme-binding protein 2	protein	20	65% helix, 0% strand	Q9Y5Z4
F	Heme-binding protein 2	protein	21	76% helix, 0% strand	Q9Y5Z4
G	Heme-binding protein 2	protein	19	53% helix, 0% strand	Q9Y5Z4
H	Heme-binding protein 2	protein	19	89% helix, 0% strand	Q9Y5Z4

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	340	0.62	0.79	40	empty
2	333	0.60	0.78	49	empty
3	134	0.48	0.78	16	empty
4	78	0.46	0.82	20	empty
5	92	0.38	0.76	15	empty

Interfaces

8 interfaces between chains.

C–D · 2055 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1865 Å² buried · 23 hydrogen bonds · protein-protein
C–G · 982 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 981 Å² buried · 10 hydrogen bonds · protein-protein
D–H · 975 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3R85 · Crystal structure of human SOUL BH3 domain in complex with Bcl-xL · the same entry in another collection · chain H against H, TM-score 1.00
Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 Q07817
Every structure of UniProt Q9Y5Z4
Elsewhere: RCSB PDB 3R85 · PDBe 3R85 · UniProt Q07817 · UniProt Q9Y5Z4

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