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Structure of protease 1 from pyrococcus horikoshii co-crystallized in presence of 10 mm tb-XO4 and potassium iodide.

Analyse Structure of protease 1 from pyrococcus horikoshii co-crystallized in presence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F2H
Type: protein
Length: 1,992 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deglycase PH1704
EC: 3.5.1.124, 3.4.22.-
UniProt: O59413
Ligands: 7MT, TB, IOD
Pockets: 19 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Deglycase PH1704 (EC 3.5.1.124, 3.4.22.-)	protein	166	39% helix, 25% strand	O59413

Ligands and binding sites

7MT · Tb-Xo4 · ligand · 9 copies · chains A, B, E, F, G, I, J, K, L
TB · Terbium(iii) ion · metal · 9 copies · chains C, D, E, F, H, K
IOD · Iodide ion · ion · 11 copies · chains A, B, C, E, F, G, H, I, J, K, L

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

Pockets

19 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.59	0.81	30	empty
2	258	0.58	0.79	37	empty
3	345	0.51	0.72	32	empty
4	111	0.49	0.81	23	empty
5	117	0.46	0.79	19	empty

Interfaces

14 interfaces between chains.

G–H · 889 Å² buried · 20 hydrogen bonds · protein-protein
K–L · 888 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 886 Å² buried · 19 hydrogen bonds · protein-protein
I–J · 885 Å² buried · 19 hydrogen bonds · protein-protein
A–F · 882 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6F2H · Structure of Protease 1 from Pyrococcus horikoshii co-crystallized in presence of 10 mM… · the same entry in another collection · chain L against L, 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 O59413
Elsewhere: RCSB PDB 6F2H · PDBe 6F2H · UniProt O59413

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