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Crystal structure of a truncated human tudor-sn

Analyse Crystal structure of a truncated human tudor-sn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BDL
Type: protein
Length: 537 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Staphylococcal nuclease domain-containing protein 1
EC: 3.1.31.1
UniProt: Q7KZF4
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1)	protein	537	29% helix, 31% strand	Q7KZF4

Ligands and binding sites

CIT · Citric acid · additive · 4 copies · chains A

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

Pockets

9 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	235	0.63	0.82	37	empty
2	292	0.62	0.79	38	CIT
3	181	0.46	0.74	23	empty
4	180	0.44	0.74	21	empty
5	64	0.41	0.81	15	empty

Compared structures

3BDL · Crystal structure of a truncated human Tudor-SN · the same entry in another collection · chain A against A, TM-score 1.00
Q7KZF4 · AlphaFold monomer V2.0 prediction for staphylococcal nuclease domain- containing protein… · a predicted model of the same protein · chain A 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 Q7KZF4
Elsewhere: RCSB PDB 3BDL · PDBe 3BDL · UniProt Q7KZF4

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