MolNFT v1 · #72133 · protein

Crystal structure of zinc-bound natrin from naja atra

3MZ8 · Natrin-1: “Crystal structure of zinc-bound natrin from naja atra”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.71). MolNFT v1 #72133 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MZ8
Type: protein
Length: 440 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Natrin-1
UniProt: Q7T1K6
Ligands: ZN
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Natrin-1	protein	220	34% helix, 19% strand	Q7T1K6

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

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	1091	0.71	0.75	78	empty
2	275	0.51	0.74	38	empty
3	219	0.48	0.74	30	empty

Interfaces

1 interface between chains.

A–B · 296 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

3MZ8 · Crystal Structure of Zinc-Bound Natrin From Naja atra · the same entry in another collection · chain A against A, TM-score 1.00
Q7T1K6 · AlphaFold monomer V2.0 prediction for cysteine-rich venom protein natrin-1 (Q7T1K6) · 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 Q7T1K6
Elsewhere: RCSB PDB 3MZ8 · PDBe 3MZ8 · UniProt Q7T1K6

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