Research workbench

Three dimensional structure of the small metal binding protein, smbp

Analyse Three dimensional structure of the small metal binding protein, smbp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U8V
Type: protein
Length: 166 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metal-binding protein smbp
UniProt: Q82S91
Ligands: NI
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Metal-binding protein smbp	protein	83	87% helix, 0% strand	Q82S91

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	161	0.48	0.77	29	empty

Interfaces

1 interface between chains.

A–B · 369 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3U8V · Three dimensional structure of the Small Metal Binding Protein, SMBP · the same entry in another collection · chain A against A, TM-score 1.00
Q82S91 · AlphaFold monomer V2.0 prediction for metal-binding protein smbp (Q82S91) · 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 Q82S91
Elsewhere: RCSB PDB 3U8V · PDBe 3U8V · UniProt Q82S91

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