Research workbench

Crystal structure of the PH0510 protein from pyrococcus horikoshii OT3

Analyse Crystal structure of the PH0510 protein from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DEC
Type: protein
Length: 650 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 325AA long hypothetical protein
UniProt: O58246
Ligands: NA
Pockets: 7 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	325AA long hypothetical protein	protein	325	46% helix, 17% strand	O58246

Ligands and binding sites

NA · Sodium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

7 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	610	0.88	0.92	66	EDO
2	114	0.78	0.97	26	NA, EDO
3	147	0.76	0.94	31	empty
4	141	0.61	0.84	23	empty
5	145	0.59	0.83	22	empty

Interfaces

1 interface between chains.

A–B · 2756 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

2DEC · Crystal Structure of the PH0510 protein from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00

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 O58246
Elsewhere: RCSB PDB 2DEC · PDBe 2DEC · UniProt O58246

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.