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Crystal structure of the nicotiana glutinosa ribonuclease nw

Analyse Crystal structure of the nicotiana glutinosa ribonuclease nw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IYB
Type: protein
Length: 416 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease
EC: 3.1.-.-
UniProt: Q7XZV5
Ligands: 5GP
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease (EC 3.1.-.-)	protein	208	31% helix, 19% strand	Q7XZV5

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

3 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	176	0.55	0.80	26	empty
2	100	0.36	0.74	20	empty
3	62	0.29	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 631 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

1IYB · Crystal Structure of the Nicotiana glutinosa Ribonuclease NW · 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 Q7XZV5
Elsewhere: RCSB PDB 1IYB · PDBe 1IYB · UniProt Q7XZV5

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