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Crystal structure of alpha-beta foldamer 4C in complex with BCL-xl

Analyse Crystal structure of alpha-beta foldamer 4C 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: 4A1W
Type: protein
Length: 634 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1; Alpha-beta-foldamer 2C
UniProt: Q07817
Ligands: NH2
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 6 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	141	76% helix, 0% strand	Q07817
B	BCL-2-like protein 1	protein	144	76% helix, 0% strand	Q07817
C	BCL-2-like protein 1	protein	138	78% helix, 0% strand	Q07817
D	BCL-2-like protein 1	protein	141	76% helix, 0% strand	Q07817
P, R	Alpha-beta-foldamer 2C	protein	17	88% helix, 0% strand	—
Q, S	Alpha-beta-foldamer 2C	protein	18	89% helix, 0% strand	—

Ligands and binding sites

NH2 · Amino group · ion · 4 copies · chains P, A, B, Q, R, D, S

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	224	0.61	0.81	23	empty
2	230	0.60	0.80	23	empty
3	304	0.60	0.79	46	empty
4	224	0.56	0.79	29	empty
5	125	0.44	0.77	17	empty

Interfaces

14 interfaces between chains.

A–D · 2218 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 2157 Å² buried · 22 hydrogen bonds · protein-protein
C–R · 1068 Å² buried · 9 hydrogen bonds · protein-protein
A–P · 1054 Å² buried · 12 hydrogen bonds · protein-protein
D–S · 939 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (nonstandard).

Compared structures

4A1W · Crystal structure of alpha-beta foldamer 4c in complex with Bcl-xL · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.81

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
Elsewhere: RCSB PDB 4A1W · PDBe 4A1W · UniProt Q07817

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