MolNFT v1 · #72701 · protein

Crystal structure of ap endonuclease, family 2 from brucella melitensis

3NGF: “Crystal structure of ap endonuclease, family 2 from brucella melitensis”. X-ray diffraction, 1 ligand (MN), 2 pockets (best druggability 0.53). MolNFT v1 #72701 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NGF
Type: protein
Length: 518 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ap endonuclease, family 2
EC: 5.3.1.22
UniProt: Q2YLA2
Ligands: MN
Pockets: 2 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ap endonuclease, family 2 (EC 5.3.1.22)	protein	258	41% helix, 16% strand	Q2YLA2
B	Ap endonuclease, family 2 (EC 5.3.1.22)	protein	260	40% helix, 16% strand	Q2YLA2

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

2 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	101	0.53	0.84	25	empty
2	99	0.52	0.83	23	empty

Interfaces

1 interface between chains.

A–B · 799 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3NGF · Crystal structure of AP endonuclease, family 2 from Brucella melitensis · 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 Q2YLA2
Elsewhere: RCSB PDB 3NGF · PDBe 3NGF · UniProt Q2YLA2

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