Research workbench

MRE11 dimer in complex with small molecule modulator pfmi

Analyse MRE11 dimer in complex with small molecule modulator pfmi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X1Y
Type: protein
Length: 654 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease sbccd subunit D
UniProt: Q9X1X0
Ligands: UKV
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nuclease sbccd subunit D	protein	327	28% helix, 28% strand	Q9X1X0

Ligands and binding sites

UKV · (5Z)-5-[(3-methoxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one · ligand · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

6 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	687	0.74	0.80	79	MES, UKV
2	412	0.70	0.81	51	MES, UKV
3	141	0.49	0.79	21	empty
4	69	0.33	0.75	20	empty
5	68	0.30	0.74	17	empty

Compared structures

6X1Y · Mre11 dimer in complex with small molecule modulator PFMI · the same entry in another collection · chain A against A, 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 Q9X1X0
Elsewhere: RCSB PDB 6X1Y · PDBe 6X1Y · UniProt Q9X1X0

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