MolNFT v1 · #139474 · protein

Escherichia COLI. RNase R

5XGU · Ribonuclease R: “Escherichia COLI. RNase R”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.78). MolNFT v1 #139474 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XGU
Type: protein
Length: 1,250 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease R
EC: 3.1.13.1
UniProt: H4USN4
Ligands: MG
Pockets: 15 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Ribonuclease R (EC 3.1.13.1)	protein	619	32% helix, 29% strand	H4USN4
A	Ribonuclease R (EC 3.1.13.1)	protein	631	32% helix, 30% strand	H4USN4

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1149	0.78	0.80	84	empty
2	840	0.67	0.74	76	empty
3	827	0.66	0.73	74	empty
4	295	0.58	0.78	27	empty
5	298	0.58	0.77	33	empty

Interfaces

1 interface between chains.

B–A · 309 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5XGU · Escherichia coli. RNase R · the same entry in another collection · chain B against B, 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 H4USN4
Elsewhere: RCSB PDB 5XGU · PDBe 5XGU · UniProt H4USN4

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