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Crystal structure of a pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase

Analyse Crystal structure of a pyrococcus horikoshii protein with similarities to 2'5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VDX
Type: protein
Length: 184 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein PH0099
EC: 6.5.1.3
UniProt: O57823
Ligands: CL
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein PH0099 (EC 6.5.1.3)	protein	184	30% helix, 45% strand	O57823

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	178	0.51	0.77	20	CL
2	135	0.47	0.78	24	empty

Compared structures

1VDX · Crystal Structure of a Pyrococcus horikoshii protein with similarities to 2'5' RNA-ligase · the same entry in another collection · chain A against A, TM-score 1.00
O57823 · AlphaFold monomer V2.0 prediction for RNA 2',3'-cyclic phosphodiesterase (O57823) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O57823
Elsewhere: RCSB PDB 1VDX · PDBe 1VDX · UniProt O57823

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