MolNFT v1 · #14365 · protein + DNA

Flpe-holliday junction complex

1M6X · Symmetrized frt site: “Flpe-holliday junction complex”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #14365 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1M6X
Type: protein + DNA
Length: 1,728 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Symmetrized frt site; Flp recombinase
UniProt: P03870
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F	Symmetrized frt site	dna	13	—	—
I, J	Symmetrized frt site	dna	19	—	—
G, H	Symmetrized frt site	dna	32	—	—
A	Flp recombinase	protein	399	50% helix, 13% strand	P03870
B	Flp recombinase	protein	401	49% helix, 13% strand	P03870
C, D	Flp recombinase	protein	400	50% helix, 14% strand	P03870

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	465	0.77	0.86	55	empty
2	786	0.76	0.81	72	empty
3	519	0.75	0.83	59	empty
4	683	0.75	0.81	77	empty
5	881	0.75	0.79	84	empty

Interfaces

27 interfaces between chains.

A–D · 1719 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1712 Å² buried · 18 hydrogen bonds · protein-protein
H–D · 1229 Å² buried · 31 hydrogen bonds · protein-nucleic
G–C · 1154 Å² buried · 26 hydrogen bonds · protein-nucleic
E–A · 1039 Å² buried · 22 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

1M6X · Flpe-Holliday Junction Complex · the same entry in another collection · chain B against B, TM-score 1.00
P03870 · AlphaFold monomer V2.0 prediction for site-specific recombinase flp (P03870) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P03870
Elsewhere: RCSB PDB 1M6X · PDBe 1M6X · UniProt P03870

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