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Vaccinia virus F1L bound to bim BH3

Analyse Vaccinia virus F1L bound to bim BH3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D2M
Type: protein
Length: 315 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein F1; BCL-2-like protein 11
UniProt: O57173, O43521
Ligands: CL
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein F1	protein	136	80% helix, 0% strand	O57173
B	BCL-2-like protein 11	protein	22	91% helix, 0% strand	O43521
D	BCL-2-like protein 11	protein	21	90% helix, 0% strand	O43521

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, C
MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, C

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

Pockets

2 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	245	0.75	0.89	37	MRD, CL
2	51	0.27	0.74	11	empty

Interfaces

3 interfaces between chains.

A–C · 3010 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 957 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 939 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (artifact).

Compared structures

4D2M · Vaccinia Virus F1L bound to Bim BH3 · the same entry in another collection · chain A against A, TM-score 1.00
O43521 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 11 (O43521) · a predicted model of the same protein · chain D against A, TM-score 0.67

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 O57173
Every structure of UniProt O43521
Elsewhere: RCSB PDB 4D2M · PDBe 4D2M · UniProt O57173 · UniProt O43521

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