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Arbitrium peptide receptor from spbeta phage

Analyse Arbitrium peptide receptor from spbeta phage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HP5
Type: protein
Length: 784 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SPBC2 prophage-derived uncharacterized protein yopk; Gly-met-pro-arg-gly-ala
UniProt: O31927
Ligands: SO4
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	SPBC2 prophage-derived uncharacterized protein yopk	protein	386	72% helix, 0% strand	O31927
C, D	Gly-met-pro-arg-gly-ala	protein	6	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 19 copies · chains A, B

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	403	0.66	0.79	41	empty
2	658	0.65	0.75	43	empty
3	388	0.65	0.79	40	empty
4	405	0.63	0.77	52	empty
5	65	0.36	0.78	14	empty

Interfaces

3 interfaces between chains.

A–B · 818 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 593 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 587 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified (engineered).

Compared structures

6HP5 · Arbitrium peptide receptor from spbeta phage · the same entry in another collection · chain A against A, TM-score 1.00
O31927 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived uncharacterized protein… · a predicted model of the same protein · chain A against A, TM-score 0.91

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 O31927
Elsewhere: RCSB PDB 6HP5 · PDBe 6HP5 · UniProt O31927

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