MolNFT v1 · #169087 · protein

X-ray structure of a chimeric parde toxin-antitoxin complex from mesorhizobium opportunistum

6X0A · Plasmid stabilization system: “X-ray structure of a chimeric parde toxin-antitoxin complex from mesorhizobium opportunistum”. X-ray diffraction, 1 ligand (P4G), 20 pockets (best druggability 0.73). MolNFT v1 #169087 on GenesisL1: 3D…

PDB: 6X0A
Type: protein
Length: 3,158 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasmid stabilization system; Putative addiction module antidote protein, COPG/ARC/METJ…
UniProt: F7Y4W0, F7YBW8, F7Y4V9
Ligands: P4G
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 9 distinct chains · 58% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, G, H, J, K, L, N, O, P, Q, R	Plasmid stabilization system	protein	91	40% helix, 29% strand	F7Y4W0
C	Plasmid stabilization system	protein	92	39% helix, 28% strand	F7Y4W0
I	Plasmid stabilization system	protein	88	41% helix, 24% strand	F7Y4W0
M	Plasmid stabilization system	protein	90	41% helix, 28% strand	F7Y4W0
a, b, c, p	Putative addiction module antidote protein, COPG/ARC/METJ family chimera	protein	87	72% helix, 8% strand	F7YBW8, F7Y4V9
d, f, k, m, n, r	Putative addiction module antidote protein, COPG/ARC/METJ family chimera	protein	85	72% helix, 2% strand	F7YBW8, F7Y4V9
e, h	Putative addiction module antidote protein, COPG/ARC/METJ family chimera	protein	79	80% helix, 3% strand	F7YBW8, F7Y4V9
g, l, q	Putative addiction module antidote protein, COPG/ARC/METJ family chimera	protein	86	70% helix, 6% strand	F7YBW8, F7Y4V9
i, j, o	Putative addiction module antidote protein, COPG/ARC/METJ family chimera	protein	83	75% helix, 0% strand	F7YBW8, F7Y4V9

Ligands and binding sites

P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 10 copies · chains A, B, L, C, F, D, E, M

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1158	0.73	0.76	91	empty
2	712	0.71	0.78	71	empty
3	852	0.70	0.76	80	empty
4	807	0.68	0.75	80	empty
5	548	0.65	0.76	51	empty

Interfaces

78 interfaces between chains.

M–m · 1597 Å² buried · 16 hydrogen bonds · protein-protein
P–p · 1580 Å² buried · 15 hydrogen bonds · protein-protein
L–l · 1576 Å² buried · 14 hydrogen bonds · protein-protein
Q–q · 1575 Å² buried · 10 hydrogen bonds · protein-protein
K–k · 1574 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6X0A · X-ray structure of a chimeric ParDE toxin-antitoxin complex from Mesorhizobium… · the same entry in another collection · chain B against B, TM-score 1.00

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 F7Y4W0
Every structure of UniProt F7YBW8
Every structure of UniProt F7Y4V9
Elsewhere: RCSB PDB 6X0A · PDBe 6X0A · UniProt F7Y4W0 · UniProt F7YBW8 · UniProt F7Y4V9

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