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Crystal structure of VAPBC2 from rickettsia felis bound to a DNA fragment from their promoter

Analyse Crystal structure of VAPBC2 from rickettsia felis bound to a DNA fragment from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZVK
Type: protein + DNA
Length: 852 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin of toxin-antitoxin system; Antitoxin of toxin-antitoxin system vapb; DNA
UniProt: Q4UNB2, Q4UNB3
Pockets: 13 · best druggability 0.54

Structure

x-ray diffraction · 9 distinct chains · 42% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin of toxin-antitoxin system	protein	134	56% helix, 16% strand	Q4UNB2
B	Toxin of toxin-antitoxin system	protein	133	59% helix, 16% strand	Q4UNB2
C, D	Toxin of toxin-antitoxin system	protein	132	57% helix, 16% strand	Q4UNB2
E	Antitoxin of toxin-antitoxin system vapb	protein	57	26% helix, 46% strand	Q4UNB3
F	Antitoxin of toxin-antitoxin system vapb	protein	78	17% helix, 33% strand	Q4UNB3
G	Antitoxin of toxin-antitoxin system vapb	protein	77	17% helix, 34% strand	Q4UNB3
H	Antitoxin of toxin-antitoxin system vapb	protein	57	23% helix, 47% strand	Q4UNB3
X	DNA	dna	26	—	—
Y	DNA	dna	26	—	—

Ligands and binding sites

MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains E, H, F, G

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

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	385	0.54	0.73	46	MES
2	166	0.54	0.80	28	empty
3	345	0.53	0.74	48	MES
4	90	0.46	0.80	18	empty
5	107	0.44	0.79	19	empty

Interfaces

24 interfaces between chains.

C–G · 1776 Å² buried · 28 hydrogen bonds · protein-protein
F–G · 1760 Å² buried · 30 hydrogen bonds · protein-protein
E–H · 1645 Å² buried · 30 hydrogen bonds · protein-protein
B–F · 1474 Å² buried · 28 hydrogen bonds · protein-protein
X–Y · 1184 Å² buried · 105 hydrogen bonds · nucleic-nucleic

Compared structures

3ZVK · Crystal structure of VapBC2 from Rickettsia felis bound to a DNA fragment from their… · the same entry in another collection · chain Y against Y, TM-score 1.00
Q4UNB2 · AlphaFold monomer V2.0 prediction for ribonuclease VAPC2 (Q4UNB2) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 Q4UNB2
Every structure of UniProt Q4UNB3
Elsewhere: RCSB PDB 3ZVK · PDBe 3ZVK · UniProt Q4UNB2 · UniProt Q4UNB3

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