MolNFT v1 · #5087 · protein

Endonuclease VII (endovii) ffrom phage T4

1E7D · Recombination endonuclease VII: “Endonuclease VII (endovii) ffrom phage T4”. X-ray diffraction, 3 ligands (ZN, CA, CL), 3 pockets (best druggability 0.44). MolNFT v1 #5087 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1E7D
Type: protein
Length: 314 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Recombination endonuclease VII
EC: 3.1.22.4
UniProt: P13340
Ligands: ZN, CA, CL
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Recombination endonuclease VII (EC 3.1.22.4)	protein	157	53% helix, 9% strand	P13340

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B

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	98	0.44	0.79	21	CA
2	59	0.36	0.79	15	empty
3	64	0.30	0.75	18	CA

Interfaces

1 interface between chains.

A–B · 3523 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

1E7D · Endonuclease VII (ENDOVII) Ffrom Phage T4 · 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 P13340
Elsewhere: RCSB PDB 1E7D · PDBe 1E7D · UniProt P13340

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