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Crystal structure of staphylococcal nuclease variant V23M/T62F at cryogenic temperature

Analyse Crystal structure of staphylococcal nuclease variant V23M/T62F at cryogenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K6D
Type: protein
Length: 125 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thermonuclease
EC: 3.1.31.1
UniProt: P00644
Ligands: THP, CA, PO4
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thermonuclease (EC 3.1.31.1)	protein	125	30% helix, 31% strand	P00644

Ligands and binding sites

THP · Thymidine-3',5'-diphosphate · ligand · chains A
CA · Calcium ion · metal · chains A
PO4 · Phosphate ion · ion · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.46	0.82	16	THP

Compared structures

4K6D · Crystal structure of Staphylococcal nuclease variant V23M/T62F at cryogenic temperature · 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 4K6D · PDBe 4K6D · UniProt P00644

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