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Structure of archease from pyrococcus horikoshii

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

PDB: 4N2P
Type: protein
Length: 572 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein archease
UniProt: O59205
Ligands: CA
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein archease	protein	143	27% helix, 41% strand	O59205

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B, C, D
ACT · Acetate ion · additive · 3 copies · chains A, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B, C, A, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	67	0.70	0.96	15	MPD
2	65	0.70	0.96	15	MPD
3	53	0.38	0.81	15	empty
4	104	0.37	0.75	24	empty
5	76	0.36	0.77	20	CA

Interfaces

4 interfaces between chains.

C–D · 1774 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 1766 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 731 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 693 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4N2P · Structure of Archease from Pyrococcus horikoshii · the same entry in another collection · chain D against D, TM-score 1.00
O59205 · AlphaFold monomer V2.0 prediction for protein archease (O59205) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 O59205
Elsewhere: RCSB PDB 4N2P · PDBe 4N2P · UniProt O59205

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