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Dimer of the G-Segment Invertase bound to a DNA substrate

Analyse Dimer of the G-Segment Invertase bound to a DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M6F
Type: protein + DNA
Length: 223 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.99
Source: Enterobacteria phage Mu; SYNTHETIC CONSTRUCT
Molecule: DNA-invertase; gix site analog
UniProt: P03015
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · resolution 4.99 · 3 distinct chains · 22% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-invertase	protein	188	22% helix, 0% strand	P03015
B	gix site analog	dna	17	—	—
C	gix site analog	dna	18	—	—

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	890	0.78	0.80	53	empty
2	406	0.63	0.78	36	empty
3	143	0.46	0.77	22	empty
4	98	0.41	0.77	17	empty
5	50	0.32	0.78	14	empty

Interfaces

3 interfaces between chains.

A–B · 1106 Å² buried · 37 hydrogen bonds · protein-nucleic
A–C · 1015 Å² buried · 28 hydrogen bonds · protein-nucleic
B–C · 938 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Compared structures

4M6F · Dimer of the G-segment invertase bound to a DNA substrate · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P03015
Elsewhere: RCSB PDB 4M6F · PDBe 4M6F · UniProt P03015

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