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Divalent metal ions (zinc) bound to T5 5'-exonuclease

Analyse Divalent metal ions (zinc) bound to T5 5'-exonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1UT8
Type: protein
Length: 543 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease
EC: 3.1.11.3
UniProt: P06229
Ligands: ZN
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 59% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease (EC 3.1.11.3)	protein	271	59% helix, 11% strand	P06229
B	Exodeoxyribonuclease (EC 3.1.11.3)	protein	272	59% helix, 13% strand	P06229

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

4 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	723	0.73	0.79	64	ZN
2	1012	0.73	0.77	78	ZN
3	127	0.48	0.80	20	empty
4	93	0.37	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 996 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1UT8 · Divalent metal ions (zinc) bound to T5 5'-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 P06229
Elsewhere: RCSB PDB 1UT8 · PDBe 1UT8 · UniProt P06229

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