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Constitutively active sin recombinase catalytic domain reveals two rotational intermediates

Analyse Constitutively active sin recombinase catalytic domain reveals two rotational… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C31
Type: protein
Length: 1,501 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sin, putative plasmid resolvase dimer
UniProt: P20384
Ligands: SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, I, K	Sin, putative plasmid resolvase dimer	protein	126	46% helix, 15% strand	P20384
C, D, E, F, H, J, L	Sin, putative plasmid resolvase dimer	protein	125	46% helix, 15% strand	P20384
G	Sin, putative plasmid resolvase dimer	protein	122	45% helix, 16% strand	P20384

Ligands and binding sites

SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1088	0.81	0.82	101	empty
2	954	0.74	0.77	88	SO4
3	406	0.67	0.80	45	empty
4	302	0.66	0.82	35	empty
5	96	0.64	0.89	18	empty

Interfaces

25 interfaces between chains.

C–D · 933 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 925 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 915 Å² buried · 10 hydrogen bonds · protein-protein
I–J · 904 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 878 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 84 modified (engineered).

Compared structures

5C31 · Constitutively active Sin recombinase catalytic domain reveals two rotational… · the same entry in another collection · chain L against L, 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 P20384
Elsewhere: RCSB PDB 5C31 · PDBe 5C31 · UniProt P20384

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