MolNFT v1 · #29873 · protein + DNA

Conjugative relaxase trwc in complex with orit DNA, cooper- bound structure

1ZM5 · DNA (25-mer): “Conjugative relaxase trwc in complex with orit DNA, cooper- bound structure”. X-ray diffraction, 2 ligands (CU, SO4), 3 pockets (best druggability 0.68). MolNFT v1 #29873 on GenesisL1: 3D structure, binding sites and…

PDB: 1ZM5
Type: protein + DNA
Length: 318 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (25-mer); Trwc
UniProt: Q47673
Ligands: CU, SO4
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (25-mer)	dna	25	—	—
A	Trwc	protein	293	40% helix, 21% strand	Q47673

Ligands and binding sites

CU · Copper (II) ion · metal · chains A
SO4 · Sulfate ion · ion · chains B, A

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

Pockets

3 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	464	0.68	0.80	53	SO4, CU
2	89	0.53	0.84	17	empty
3	72	0.32	0.75	12	empty

Interfaces

1 interface between chains.

B–A · 2311 Å² buried · 71 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

1ZM5 · Conjugative Relaxase TRWC in complex with ORIT dna, cooper-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 1ZM5 · PDBe 1ZM5 · UniProt Q47673

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