MolNFT v1 · #109910 · protein

Crystal structure of addiction module from mycobacterial species

4XGR · Ribonuclease VAPC30: “Crystal structure of addiction module from mycobacterial species”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.68). MolNFT v1 #109910 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4XGR
Type: protein
Length: 623 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: 6 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 53% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, E	Ribonuclease VAPC30 (EC 3.1.-.-)	protein	128	56% helix, 13% strand	P9WF77
C	Ribonuclease VAPC30 (EC 3.1.-.-)	protein	126	56% helix, 11% strand	P9WF77
B	Antitoxin VAPB30	protein	33	39% helix, 0% strand	P9WJ35
H	Antitoxin VAPB30	protein	24	42% helix, 0% strand	P9WJ35
F	Antitoxin VAPB30	protein	24	46% helix, 0% strand	P9WJ35
D	Antitoxin VAPB30	protein	32	50% helix, 0% strand	P9WJ35

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, C

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

Pockets

6 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	785	0.68	0.75	74	empty
2	205	0.56	0.80	30	empty
3	238	0.56	0.78	29	empty
4	200	0.52	0.77	28	MG
5	195	0.49	0.76	26	empty

Interfaces

15 interfaces between chains.

G–E · 1179 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1169 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1144 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1085 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 931 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4XGR · Crystal structure of addiction module from Mycobacterial species · the same entry in another collection · chain D against D, 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 0.97
P9WJ35 · AlphaFold monomer V2.0 prediction for antitoxin VAPB30 (P9WJ35) · a predicted model of the same protein · chain D against A, TM-score 0.71

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 4XGR · PDBe 4XGR · UniProt P9WF77 · UniProt P9WJ35

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