MolNFT v1 · #139651 · protein

Crystal structure of zinc binding protein zint at 1.49 ångström from E. COLI

5XM5 · Metal-binding protein zint: “Crystal structure of zinc binding protein zint at 1.49 ångström from E. COLI”. X-ray diffraction, 2 ligands (ZN, NA), 3 pockets (best druggability 0.68). MolNFT v1 #139651 on GenesisL1: 3D structure…

PDB: 5XM5
Type: protein
Length: 374 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metal-binding protein zint
UniProt: P76344
Ligands: ZN, NA
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Metal-binding protein zint	protein	187	30% helix, 29% strand	P76344

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B
NA · Sodium ion · metal · 5 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	684	0.68	0.76	65	ZN, NA
2	469	0.67	0.79	47	ZN, NA
3	57	0.34	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 311 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5XM5 · Crystal structure of Zinc binding protein ZinT at 1.49 Angstrom from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
P76344 · AlphaFold monomer V2.0 prediction for metal-binding protein zint (P76344) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P76344
Elsewhere: RCSB PDB 5XM5 · PDBe 5XM5 · UniProt P76344

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