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The crystal structure of XC847 from xanthomonas campestris: a 3-5 oligoribonuclease of dnaq fold family with a novel opposingly-shifted helix

Analyse The crystal structure of XC847 from xanthomonas campestris: a 3-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GBZ
Type: protein
Length: 179 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligoribonuclease
EC: 3.1.-.-
UniProt: Q8P8S1
Ligands: MG
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligoribonuclease (EC 3.1.-.-)	protein	179	47% helix, 17% strand	Q8P8S1

Ligands and binding sites

MG · Magnesium ion · metal · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	184	0.46	0.75	27	MG
2	74	0.30	0.73	11	empty

Compared structures

2GBZ · The Crystal Structure of XC847 from Xanthomonas campestris: a 3-5 Oligoribonuclease of… · the same entry in another collection · chain A against A, TM-score 1.00
Q8P8S1 · AlphaFold monomer V2.0 prediction for oligoribonuclease (Q8P8S1) · 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 Q8P8S1
Elsewhere: RCSB PDB 2GBZ · PDBe 2GBZ · UniProt Q8P8S1

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