MolNFT v1 · #138927 · protein

Crystal structure of mycobacterium tuberculosis VAPC20 (RV2549C), sarcin-ricin loop cleaving toxin

5WZ4 · 23S rRNA-specific endonuclease VAPC20: “Crystal structure of mycobacterium tuberculosis VAPC20 (RV2549C), sarcin-ricin loop cleaving toxin”. X-ray diffraction, 1 pocket (best druggability 0.67). MolNFT v1 #138927 on GenesisL1: 3D…

PDB: 5WZ4
Type: protein
Length: 260 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA-specific endonuclease VAPC20
EC: 3.1.-.-
UniProt: P95004
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	23S rRNA-specific endonuclease VAPC20 (EC 3.1.-.-)	protein	130	55% helix, 12% strand	P95004

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	363	0.67	0.81	57	empty

Interfaces

1 interface between chains.

A–B · 1249 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered, oxidation).

Compared structures

5WZ4 · Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop… · the same entry in another collection · chain A against A, TM-score 1.00
P95004 · AlphaFold monomer V2.0 prediction for 23S rRNA-specific endonuclease VAPC20 (P95004) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P95004
Elsewhere: RCSB PDB 5WZ4 · PDBe 5WZ4 · UniProt P95004

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