7YA5: Apoptosis regulator Bcl-2

Name: PDB 7YA5: Crystal structure analysis of cp1 bound BCL2/G101V
Published: 2023-11-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Crystal structure analysis of cp1 bound BCL2/G101V. Determined by X-ray diffraction at 1.85 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,384
Mol. weight: 21.25 kDa
Ligands: JFF
Released: 15 Nov 2023

Explore 7YA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YA5 contains 10 α-helices and 0 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	11-25	15
α-helix	90-107	18
α-helix	109-116	8
α-helix	126-138	13
α-helix	144-163	20
α-helix	169-180	12
α-helix	181-185	5
α-helix	186-191	6
α-helix	194-202	9

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptosis regulator Bcl-2	A	protein	166	Homo sapiens	P10415 (AlphaFold model)
cp1 peptide	B	protein	12	synthetic construct

Sequence of entity 1 (A), FASTA

>7YA5_1 Apoptosis regulator Bcl-2 (chains A)
MAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDDVEENRTEAPEGTESEVVHLTLRQAV
DDFSRRYRRDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCVES
VNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGPSMR

Sequence of entity 2 (B), FASTA

>7YA5_2 cp1 peptide (chains B)
CPARYGWDYECX

Ligands and cofactors

ID	Name	Formula	Copies
JFF	(2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamo…	C19 H26 Cl N5 O6 S	1

Primary citation

Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-X L by engaging a single-residue discrepancy. Li, F., Liu, J., Liu, C. et al. Nat Commun (2024) 15:1476-1476. DOI 10.1038/s41467-024-45848-1 · PubMed

Other PDB entries of the same protein (UniProt P10415 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HTS 1.25 Å, Crystal structure of Bcl2 in complex with S-10r
6GL8 1.4 Å, Crystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746
6QGG 1.5 Å, Structure of human Bcl-2 in complex with analogue of ABT-737
9IGG 1.5 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
8HTR 1.6 Å, Crystal structure of Bcl2 in complex with S-9c
6O0K 1.62 Å, crystal structure of BCL-2 with venetoclax
9I9E 1.7 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
9O14 1.73 Å, Crystal Structure of BCL-2 in complex with a stapled BAD BH3 peptide BAD SAHB 4.2
9O16 1.73 Å, Crystal Structure of human BCL-2 (R129L) mutant in complex with a stapled BAD BH3…
6O0M 1.75 Å, crystal structure of BCL-2 F104L mutation with venetoclax
5VAU 1.75 Å, Bcl-2 complex with Beclin 1 BH3 domain
8VWX 1.77 Å, Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to Maltose-Binding Protein

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