MolNFT v1 · #62106 · protein

Crystal structure of staphylococcal nuclease variant DELTA+PHS L103K at cryogenic temperature

3E5S · Thermonuclease: “Crystal structure of staphylococcal nuclease variant DELTA+PHS L103K at cryogenic temperature”. X-ray diffraction, 2 ligands (THP, CA), 3 pockets (best druggability 0.44). MolNFT v1 #62106 on GenesisL1: 3D…

PDB: 3E5S
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thermonuclease
EC: 3.1.31.1
UniProt: P00644
Ligands: THP, CA
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Thermonuclease (EC 3.1.31.1)	protein	129	28% helix, 31% strand	P00644

Ligands and binding sites

THP · Thymidine-3',5'-diphosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	91	0.44	0.79	17	THP
2	143	0.42	0.74	18	empty
3	85	0.41	0.78	19	THP

Interfaces

1 interface between chains.

A–B · 496 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3E5S · Crystal structure of Staphylococcal nuclease variant Delta+PHS L103K at cryogenic… · 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 P00644
Elsewhere: RCSB PDB 3E5S · PDBe 3E5S · UniProt P00644

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