MolNFT v1 · #23838 · protein

Crystal structure of ribonuclease MC1 from bitter gourd seeds complexed with 5'-ump

1UCD: “Crystal structure of ribonuclease MC1 from bitter gourd seeds complexed with 5'-ump”. X-ray diffraction, 2 ligands (U5P, URA), 1 pocket (best druggability 0.31). MolNFT v1 #23838 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1UCD
Type: protein
Length: 190 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease mc
EC: 3.1.27.1
UniProt: P23540
Ligands: U5P, URA
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease mc (EC 3.1.27.1)	protein	190	38% helix, 23% strand	P23540

Ligands and binding sites

U5P · Uridine-5'-monophosphate · ligand · chains A
URA · Uracil · ligand · 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	65	0.31	0.75	19	U5P

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1UCD · Crystal structure of Ribonuclease MC1 from bitter gourd seeds complexed with 5'-UMP · the same entry in another collection · chain A against A, TM-score 1.00
P23540 · AlphaFold monomer V2.0 prediction for ribonuclease mc (P23540) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P23540
Elsewhere: RCSB PDB 1UCD · PDBe 1UCD · UniProt P23540

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