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Crystal structure of a serine recombinase- DNA regulatory complex

Analyse Crystal structure of a serine recombinase- DNA regulatory complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R0Q
Type: protein + DNA
Length: 892 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative transposon TN552 DNA-invertase BIN3; 31-mer
UniProt: P20384
Ligands: SO4
Pockets: 20 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E	Putative transposon TN552 DNA-invertase BIN3	protein	193	56% helix, 10% strand	P20384
D, F	Putative transposon TN552 DNA-invertase BIN3	protein	191	49% helix, 10% strand	P20384
A, G	31-mer	dna	31	—	—
B, H	31-mer	dna	31	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.56	0.75	31	empty
2	324	0.55	0.75	28	empty
3	263	0.52	0.75	35	SO4
4	163	0.48	0.77	17	SO4
5	67	0.38	0.79	15	empty

Interfaces

14 interfaces between chains.

E–F · 1575 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1533 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1312 Å² buried · 100 hydrogen bonds · nucleic-nucleic
G–H · 1311 Å² buried · 101 hydrogen bonds · nucleic-nucleic
E–G · 941 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

2R0Q · Crystal structure of a serine recombinase- DNA regulatory complex · the same entry in another collection · chain F against F, TM-score 1.00
P20384 · AlphaFold monomer V2.0 prediction for putative transposon TN552 DNA- invertase BIN3… · a predicted model of the same protein · chain F against A, TM-score 0.56

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 P20384
Elsewhere: RCSB PDB 2R0Q · PDBe 2R0Q · UniProt P20384

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