MolNFT v1 · #76143 · protein

BAKBH3 in complex with sja

3QBR · SJCHGC06286 protein: “BAKBH3 in complex with sja”. X-ray diffraction, 4 pockets (best druggability 0.51). MolNFT v1 #76143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QBR
Type: protein
Length: 371 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SJCHGC06286 protein; BCL-2 homologous ANTAGONIST/KILLER
UniProt: Q5BWX6, Q16611
Pockets: 4 · best druggability 0.51

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SJCHGC06286 protein	protein	163	75% helix, 0% strand	Q5BWX6
B	BCL-2 homologous ANTAGONIST/KILLER	protein	24	79% helix, 0% strand	Q16611
X	SJCHGC06286 protein	protein	161	69% helix, 0% strand	Q5BWX6
Y	BCL-2 homologous ANTAGONIST/KILLER	protein	23	78% helix, 0% strand	Q16611

Ligands and binding sites

NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains X, Y

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

Pockets

4 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	60	0.51	0.85	16	empty
2	195	0.48	0.76	30	empty
3	59	0.30	0.75	16	empty
4	51	0.26	0.73	12	empty

Interfaces

3 interfaces between chains.

A–B · 973 Å² buried · 10 hydrogen bonds · protein-protein
X–Y · 902 Å² buried · 5 hydrogen bonds · protein-protein
A–X · 427 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3QBR · BakBH3 in complex with sjA · the same entry in another collection · chain A against A, TM-score 1.00
Q16611 · AlphaFold monomer V2.0 prediction for BCL-2 homologous ANTAGONIST/KILLER (Q16611) · a predicted model of the same protein · chain Y against A, TM-score 0.69

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 Q5BWX6
Every structure of UniProt Q16611
Elsewhere: RCSB PDB 3QBR · PDBe 3QBR · UniProt Q5BWX6 · UniProt Q16611

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