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Crystal structure of DNA bound vapbc from salmonella typhimurium

Analyse Crystal structure of DNA bound vapbc from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IFM
Type: protein + DNA
Length: 854 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA(FMET)-specific endonuclease vapc; Antitoxin vapb; DNA forward (27-mer); DNA backward…
EC: 3.1.-.-
UniProt: Q8ZM86, Q7CPV2
Pockets: 9 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, C, G	TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-)	protein	132	56% helix, 9% strand	Q8ZM86
B, F, H, D	Antitoxin vapb	protein	68	7% helix, 35% strand	Q7CPV2
M	DNA forward (27-mer)	dna	27	—	—
N	DNA backward (27-mer)	dna	27	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	881	0.71	0.76	96	empty
2	605	0.64	0.75	60	empty
3	177	0.48	0.76	31	empty
4	100	0.41	0.77	19	empty
5	58	0.39	0.80	15	empty

Interfaces

28 interfaces between chains.

B–H · 1887 Å² buried · 39 hydrogen bonds · protein-protein
F–D · 1839 Å² buried · 30 hydrogen bonds · protein-protein
E–F · 1574 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1558 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 1415 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6IFM · Crystal structure of DNA bound VapBC from Salmonella typhimurium · the same entry in another collection · chain N against N, TM-score 1.00
Q8ZM86 · AlphaFold monomer V2.0 prediction for TRNA(FMET)-specific endonuclease vapc (Q8ZM86) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q7CPV2 · AlphaFold monomer V2.0 prediction for antitoxin vapb (Q7CPV2) · a predicted model of the same protein · chain B against A, TM-score 0.61

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 Q8ZM86
Every structure of UniProt Q7CPV2
Elsewhere: RCSB PDB 6IFM · PDBe 6IFM · UniProt Q8ZM86 · UniProt Q7CPV2

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