MolNFT v1 · #80254 · protein

Structure of an oligoribonuclease (orn) from coxiella burnetii

3TR8: “Structure of an oligoribonuclease (orn) from coxiella burnetii”. X-ray diffraction, 2 ligands (MN, MG), 4 pockets (best druggability 0.63). MolNFT v1 #80254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3TR8
Type: protein
Length: 368 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligoribonuclease
EC: 3.1.-.-
UniProt: Q83C93
Ligands: MN, MG
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Oligoribonuclease (EC 3.1.-.-)	protein	184	43% helix, 16% strand	Q83C93

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A, B

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

Pockets

4 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	392	0.63	0.78	32	MN, MG
2	326	0.61	0.78	27	MN, MG
3	121	0.54	0.83	27	empty
4	82	0.43	0.80	19	empty

Interfaces

1 interface between chains.

A–B · 1734 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 1 disulfide (engineered, disulfide).

Compared structures

3TR8 · Structure of an oligoribonuclease (orn) from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
Q83C93 · AlphaFold monomer V2.0 prediction for oligoribonuclease (Q83C93) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q83C93
Elsewhere: RCSB PDB 3TR8 · PDBe 3TR8 · UniProt Q83C93

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