Research workbench

Conjugative relaxase trwc in complex with orit DNA. metal- bound structure

Analyse Conjugative relaxase trwc in complex with orit DNA. metal- bound structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1S6M
Type: protein + DNA
Length: 313 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (25-mer); Trwc
UniProt: Q47673
Ligands: NI
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (25-mer)	dna	25	—	—
A	Trwc	protein	288	39% helix, 21% strand	Q47673

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A

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

Pockets

5 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	474	0.72	0.82	37	empty
2	102	0.54	0.84	21	empty
3	120	0.49	0.80	29	empty
4	62	0.32	0.77	12	empty
5	69	0.32	0.75	13	empty

Interfaces

1 interface between chains.

B–A · 2277 Å² buried · 47 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

1S6M · Conjugative Relaxase Trwc In Complex With Orit DNA. Metal-Bound Structure · 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 Q47673
Elsewhere: RCSB PDB 1S6M · PDBe 1S6M · UniProt Q47673

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.