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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: 6HP3
Type: protein
Length: 3,088 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SPBC2 prophage-derived uncharacterized protein yopk
UniProt: O31927
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	SPBC2 prophage-derived uncharacterized protein yopk	protein	386	72% helix, 0% strand	O31927

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	480	0.84	0.91	38	empty
2	786	0.81	0.84	49	empty
3	639	0.80	0.85	43	empty
4	921	0.79	0.81	93	empty
5	744	0.78	0.82	47	empty

Interfaces

9 interfaces between chains.

A–B · 1446 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1294 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1243 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1174 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 698 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 120 modified (engineered).

Compared structures

6HP3 · Arbitrium peptide receptor from spbeta phage · the same entry in another collection · chain H against H, 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 0.95

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 6HP3 · PDBe 6HP3 · UniProt O31927

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