Research workbench

Orf virus encoded BCL-2 homolog ORFV125 in complex with puma BH3 peptide

Analyse Orf virus encoded BCL-2 homolog ORFV125 in complex with puma BH3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7P0U
Type: protein
Length: 616 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apoptosis inhibitor; Activator of apoptosis harakiri
UniProt: A0A0R8HV90, O00198
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 8 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apoptosis inhibitor	protein	134	77% helix, 0% strand	A0A0R8HV90
U	Activator of apoptosis harakiri	protein	26	73% helix, 0% strand	O00198
B	Apoptosis inhibitor	protein	132	78% helix, 0% strand	A0A0R8HV90
C	Activator of apoptosis harakiri	protein	24	88% helix, 0% strand	O00198
D	Apoptosis inhibitor	protein	128	77% helix, 0% strand	A0A0R8HV90
E	Activator of apoptosis harakiri	protein	22	91% helix, 0% strand	O00198
F	Apoptosis inhibitor	protein	129	80% helix, 0% strand	A0A0R8HV90
G	Activator of apoptosis harakiri	protein	21	90% helix, 0% strand	O00198

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, F
GOL · Glycerol · additive · 3 copies · chains A, C

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.75	0.91	23	EDO
2	489	0.61	0.74	48	empty
3	302	0.54	0.75	29	empty
4	300	0.53	0.74	27	empty
5	97	0.52	0.84	19	empty

Interfaces

11 interfaces between chains.

B–F · 2894 Å² buried · 31 hydrogen bonds · protein-protein
A–U · 1158 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 973 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 862 Å² buried · 6 hydrogen bonds · protein-protein
F–G · 853 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7P0U · ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide · the same entry in another collection · chain G against G, TM-score 1.00
O00198 · AlphaFold monomer V2.0 prediction for activator of apoptosis harakiri (O00198) · a predicted model of the same protein · chain E against A, TM-score 0.82

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 A0A0R8HV90
Every structure of UniProt O00198
Elsewhere: RCSB PDB 7P0U · PDBe 7P0U · UniProt A0A0R8HV90 · UniProt O00198

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