MolNFT v1 · #145229 · protein + DNA

Proteus vulgaris higa antitoxin bound to DNA

6CHV · Antitoxin higa: “Proteus vulgaris higa antitoxin bound to DNA”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.83). MolNFT v1 #145229 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CHV
Type: protein + DNA
Length: 659 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antitoxin higa; PHIGCRYST3; PHIGCRYST4
UniProt: Q7A224
Ligands: MG
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 62% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antitoxin higa	protein	89	62% helix, 0% strand	Q7A224
C	Antitoxin higa	protein	88	65% helix, 0% strand	Q7A224
I, E, K	PHIGCRYST3	dna	21	—	—
J, F, L	PHIGCRYST4	dna	21	—	—
B	Antitoxin higa	protein	88	63% helix, 0% strand	Q7A224
D	Antitoxin higa	protein	91	62% helix, 0% strand	Q7A224
G	Antitoxin higa	protein	91	60% helix, 0% strand	Q7A224
H	Antitoxin higa	protein	86	62% helix, 0% strand	Q7A224

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains F, K, L

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1124	0.83	0.84	100	empty
2	388	0.80	0.89	59	empty
3	858	0.71	0.77	49	empty
4	723	0.69	0.77	46	empty
5	719	0.68	0.76	43	empty

Interfaces

27 interfaces between chains.

B–D · 1444 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 1421 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1413 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 922 Å² buried · 82 hydrogen bonds · nucleic-nucleic
E–F · 921 Å² buried · 92 hydrogen bonds · nucleic-nucleic

Compared structures

6CHV · Proteus vulgaris HigA antitoxin bound to DNA · the same entry in another collection · chain L against L, 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 Q7A224
Elsewhere: RCSB PDB 6CHV · PDBe 6CHV · UniProt Q7A224

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