MolNFT v1 · #189125 · protein

Crystal structure of apo-np exonuclease C409A

7V3A · Nucleoprotein: “Crystal structure of apo-np exonuclease C409A”. X-ray diffraction, 2 ligands (ZN, MG), 6 pockets (best druggability 0.50). MolNFT v1 #189125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7V3A
Type: protein
Length: 409 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, MG
Pockets: 6 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein (EC 3.1.13.-)	protein	207	38% helix, 20% strand	P13699
B	Nucleoprotein (EC 3.1.13.-)	protein	202	37% helix, 19% strand	P13699

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium 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	96	0.50	0.82	17	empty
2	117	0.44	0.77	17	empty
3	164	0.40	0.73	23	MG
4	110	0.39	0.76	23	empty
5	111	0.36	0.74	17	MG

Interfaces

1 interface between chains.

A–B · 429 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7V3A · Crystal structure of apo-NP exonuclease C409A · 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 7V3A · PDBe 7V3A · UniProt P13699

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