MolNFT v1 · #111219 · protein

Crystal structure of eukaryotic MRE11 catalytic domain from chaetomium thermophilum

4YKE: “Crystal structure of eukaryotic MRE11 catalytic domain from chaetomium thermophilum”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.63). MolNFT v1 #111219 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4YKE
Type: protein
Length: 809 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRE11
UniProt: G0RYR3
Ligands: MN
Pockets: 11 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRE11	protein	404	24% helix, 24% strand	G0RYR3
B	MRE11	protein	405	23% helix, 24% strand	G0RYR3

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.63	0.82	36	empty
2	159	0.62	0.85	30	empty
3	157	0.62	0.84	27	empty
4	78	0.54	0.86	26	empty
5	91	0.48	0.81	20	empty

Interfaces

1 interface between chains.

A–B · 1545 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4YKE · Crystal structure of eukaryotic Mre11 catalytic domain from Chaetomium thermophilum · 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 G0RYR3
Elsewhere: RCSB PDB 4YKE · PDBe 4YKE · UniProt G0RYR3

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