MolNFT v1 · #109909 · protein

Crystal structure of addiction module from mycobacterial species

4XGQ · Ribonuclease VAPC30: “Crystal structure of addiction module from mycobacterial species”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.69). MolNFT v1 #109909 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4XGQ
Type: protein
Length: 648 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease VAPC30; Antitoxin VAPB30
EC: 3.1.-.-
UniProt: P9WF77, P9WJ35
Ligands: MG
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, C, G	Ribonuclease VAPC30 (EC 3.1.-.-)	protein	132	55% helix, 12% strand	P9WF77
B, F, D, H	Antitoxin VAPB30	protein	30	47% helix, 0% strand	P9WJ35

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, E, C

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	799	0.69	0.75	79	empty
2	254	0.58	0.79	28	empty
3	271	0.55	0.77	31	MG
4	215	0.51	0.77	32	empty
5	167	0.49	0.78	24	empty

Interfaces

15 interfaces between chains.

A–C · 1192 Å² buried · 22 hydrogen bonds · protein-protein
E–G · 1166 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1051 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1046 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1033 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4XGQ · Crystal structure of addiction module from Mycobacterial species · the same entry in another collection · chain H against H, TM-score 1.00
P9WF77 · AlphaFold monomer V2.0 prediction for ribonuclease VAPC30 (P9WF77) · a predicted model of the same protein · chain A against A, TM-score 0.96
P9WJ35 · AlphaFold monomer V2.0 prediction for antitoxin VAPB30 (P9WJ35) · a predicted model of the same protein · chain B against A, TM-score 0.66

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 P9WF77
Every structure of UniProt P9WJ35
Elsewhere: RCSB PDB 4XGQ · PDBe 4XGQ · UniProt P9WF77 · UniProt P9WJ35

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