MolNFT v1 · #149480 · protein + DNA

Tran, a repressor of an enterococcus conjugative type IV secretion system

6G1T · AM32: “Tran, a repressor of an enterococcus conjugative type IV secretion system”. X-ray diffraction, 1 pocket (best druggability 0.38). MolNFT v1 #149480 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6G1T
Type: protein + DNA
Length: 176 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AM32; DNA (34-mer)
Pockets: 1 · best druggability 0.38

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AM32	protein	115	45% helix, 19% strand	—
E	DNA (34-mer)	dna	32	—	—
D	DNA (34-mer)	dna	29	—	—

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.38	0.81	17	empty

Interfaces

3 interfaces between chains.

E–D · 1312 Å² buried · 121 hydrogen bonds · nucleic-nucleic
A–D · 917 Å² buried · 22 hydrogen bonds · protein-nucleic
A–E · 897 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

6G1T · TraN, a repressor of an Enterococcus conjugative type IV secretion system · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 6G1T · PDBe 6G1T

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