MolNFT v1 · #116650 · protein

Crystal structure of crn-4-mes complex

5DK5 · Cell death-related nuclease 4: “Crystal structure of crn-4-mes complex”. X-ray diffraction, 2 ligands (ZN, MG), 7 pockets (best druggability 0.65). MolNFT v1 #116650 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DK5
Type: protein
Length: 589 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell death-related nuclease 4
EC: 3.1.-.-
UniProt: Q10905
Ligands: ZN, MG
Pockets: 7 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cell death-related nuclease 4 (EC 3.1.-.-)	protein	294	37% helix, 18% strand	Q10905
B	Cell death-related nuclease 4 (EC 3.1.-.-)	protein	295	37% helix, 18% strand	Q10905

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
IPA · Isopropyl alcohol · additive · 7 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

7 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	436	0.65	0.78	50	MES, MG, IPA
2	398	0.65	0.78	43	MES, MG
3	114	0.52	0.81	18	empty
4	143	0.50	0.79	24	empty
5	149	0.46	0.77	22	empty

Interfaces

1 interface between chains.

A–B · 955 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5DK5 · Crystal structure of CRN-4-MES complex · the same entry in another collection · chain A against A, TM-score 1.00
Q10905 · AlphaFold monomer V2.0 prediction for cell death-related nuclease 4 (Q10905) · a predicted model of the same protein · chain B 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 Q10905
Elsewhere: RCSB PDB 5DK5 · PDBe 5DK5 · UniProt Q10905

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