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Crystal structure of apo-np exonuclease

Analyse Crystal structure of apo-np exonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V37
Type: protein
Length: 403 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
EC: 3.1.13.-
UniProt: P13699
Ligands: ZN
Pockets: 6 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein (EC 3.1.13.-)	protein	202	38% helix, 18% strand	P13699
B	Nucleoprotein (EC 3.1.13.-)	protein	201	38% helix, 20% strand	P13699

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

6 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	178	0.43	0.74	24	empty
2	124	0.41	0.75	20	empty
3	122	0.41	0.76	19	empty
4	88	0.34	0.74	16	empty
5	57	0.32	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 451 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7V37 · Crystal structure of apo-NP exonuclease · 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 P13699
Elsewhere: RCSB PDB 7V37 · PDBe 7V37 · UniProt P13699

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