MolNFT v1 · #101988 · protein

Crystal structure of a N-tagged nuclease

4O87: “Crystal structure of a N-tagged nuclease”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.59). MolNFT v1 #101988 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4O87
Type: protein
Length: 637 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-tagged nuclease
UniProt: Q707V3
Ligands: SO4
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-tagged nuclease	protein	318	49% helix, 15% strand	Q707V3
B	N-tagged nuclease	protein	319	49% helix, 14% strand	Q707V3

Ligands and binding sites

SO4 · Sulfate ion · ion · 27 copies · chains A, B
CIT · Citric acid · additive · 2 copies · chains A, B

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

Pockets

5 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	371	0.59	0.76	49	empty
2	273	0.54	0.76	33	empty
3	95	0.38	0.76	16	empty
4	60	0.34	0.77	12	empty
5	58	0.26	0.72	16	SO4

Interfaces

1 interface between chains.

A–B · 117 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4O87 · Crystal structure of a N-tagged Nuclease · 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 Q707V3
Elsewhere: RCSB PDB 4O87 · PDBe 4O87 · UniProt Q707V3

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