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Crystal structure of two covalent nucleoside derivatives of ribonuclease a

Analyse Crystal structure of two covalent nucleoside derivatives of ribonuclease a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 9RSA
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease a
EC: 3.1.27.5
UniProt: P61823
Ligands: ADU
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease a (EC 3.1.27.5)	protein	124	21% helix, 36% strand	P61823

Ligands and binding sites

ADU · 3'-deoxy-3'-acetamido-uridine · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	348	0.63	0.79	47	empty

Interfaces

1 interface between chains.

A–B · 953 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

9RSA · Crystal structure of two covalent nucleoside derivatives of ribonuclease a · 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 P61823
Elsewhere: RCSB PDB 9RSA · PDBe 9RSA · UniProt P61823

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