MolNFT v1 · #159980 · protein

Old nuclease from thermus scotoductus

6P74 · Putative ATP-dependent endonuclease of the old family: “Old nuclease from thermus scotoductus”. X-ray diffraction, 3 ligands (PT, SM, SO4), 3 pockets (best druggability 0.43). MolNFT v1 #159980 on GenesisL1: 3D structure, binding…

PDB: 6P74
Type: protein
Length: 512 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ATP-dependent endonuclease of the old family
UniProt: E8PLM2
Ligands: PT, SM, SO4
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative ATP-dependent endonuclease of the old family	protein	512	43% helix, 21% strand	E8PLM2

Ligands and binding sites

PT · Platinum (II) ion · metal · 2 copies · chains A
SM · Samarium (III) ion · metal · chains A
SO4 · Sulfate ion · ion · 8 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A

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	135	0.43	0.76	26	SO4
2	54	0.32	0.77	11	empty
3	65	0.31	0.75	21	SM

Compared structures

6P74 · OLD nuclease from Thermus Scotoductus · 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 E8PLM2
Elsewhere: RCSB PDB 6P74 · PDBe 6P74 · UniProt E8PLM2

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