MolNFT v1 · #25011 · protein

Crystal structure of RNase nt in complex with 5'-AMP

1VD1 · RNase NGR3: “Crystal structure of RNase nt in complex with 5'-AMP”. X-ray diffraction, 1 ligand (AMP), 1 pocket (best druggability 0.36). MolNFT v1 #25011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VD1
Type: protein
Length: 203 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNase NGR3
EC: 3.1.27.1
UniProt: Q9SSV1
Ligands: AMP
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNase NGR3 (EC 3.1.27.1)	protein	203	32% helix, 22% strand	Q9SSV1

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.36	0.75	21	AMP

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1VD1 · Crystal structure of RNase NT in complex with 5'-AMP · the same entry in another collection · chain A against A, 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 Q9SSV1
Elsewhere: RCSB PDB 1VD1 · PDBe 1VD1 · UniProt Q9SSV1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.