7YAA: Crystal structure analysis of cp3 bound BCLxl

Crystal structure analysis of cp3 bound BCLxl. Determined by X-ray diffraction at 1.4 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,408
Mol. weight: 17.88 kDa
Ligands: JJ9
Released: 15 Nov 2023

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

Secondary structure: helices and β-sheets

7YAA contains 11 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	2-19	18
α-helix	29-45	17
α-helix	47-54	8
α-helix	65-75	11
α-helix	82-101	20
α-helix	105-107	3
α-helix	108-118	11
α-helix	119-123	5
α-helix	124-127	4
α-helix	132-140	9

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bcl-2-like protein 1	A	protein	141	Homo sapiens	Q07817 (AlphaFold model)
cp3 peptide	B	protein	10	synthetic construct

Sequence of entity 1 (A), FASTA

>7YAA_1 Bcl-2-like protein 1 (chains A)
MSQSNRELVVDFLSYKLSQKGYSWSQPMAAVKQALREAGDEFELRYRRAFSDLTSQLHIT
PGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLN
DHLEPWIQENGGWDTFVDLYG

Sequence of entity 2 (B), FASTA

>7YAA_2 cp3 peptide (chains B)
PIRYPWDVEC

Ligands and cofactors

ID	Name	Formula	Copies
JJ9	N-(2-acetamidoethyl)-4-(4-methanoyl-1,3-thiazol-2-yl)benzamide	C15 H15 N3 O3 S	1

Water and common crystallization additives (GOL) are not listed.

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 Q07817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7JGW 1.3 Å, Crystal structure of BCL-XL in complex with COMPOUND 1620116, CRYSTAL FORM 1
3SP7 1.4 Å, Crystal Structure of Bcl-xL bound to BM903
7LH7 1.41 Å, Crystal structure of BCL-XL in complex with a benzothiazole-based inhibitor
9IGG 1.5 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
4QVF 1.53 Å, Crystal structure of Bcl-xL in complex with BIM BH3 domain
4A1U 1.54 Å, Crystal structure of alpha-beta-foldamer 2c in complex with Bcl-xL
6VWC 1.6 Å, Crystal structure of Bcl-xL in complex with tetrahydroisoquinoline-pyridine based…
6O0K 1.62 Å, crystal structure of BCL-2 with venetoclax
3SPF 1.7 Å, Crystal Structure of Bcl-xL bound to BM501
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…

Browse structure collections

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