MolNFT v1 · #98025 · protein

A new stabilizing water structure at the substrate binding site in ribosome inactivating protein from momordica balsamina at 1.80 a resolution

4KWN · RRNA N-glycosidase: “A new stabilizing water structure at the substrate binding site in ribosome inactivating protein from…”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.48). MolNFT v1 #98025 on GenesisL1: 3D…

PDB: 4KWN
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRNA N-glycosidase
EC: 3.2.2.22
UniProt: D9J2T9
Ligands: NAG
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RRNA N-glycosidase (EC 3.2.2.22)	protein	246	43% helix, 24% strand	D9J2T9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.48	0.78	19	empty
2	70	0.33	0.75	14	empty

Modifications

Observed in the structure: 1 glycan (N-glycosylation).

Compared structures

4KWN · A new stabilizing water structure at the substrate binding site in ribosome inactivating… · 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 D9J2T9
Elsewhere: RCSB PDB 4KWN · PDBe 4KWN · UniProt D9J2T9

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