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Crystal structure of M-crystallin in the presence of nickel

Analyse Crystal structure of M-crystallin in the presence of nickel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HT9
Type: protein
Length: 168 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BETA/GAMA crystallin family protein
UniProt: Q8TMX3
Ligands: MG, NI
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	BETA/GAMA crystallin family protein	protein	84	11% helix, 49% strand	Q8TMX3

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · chains A, B
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · 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	63	0.39	0.79	12	empty

Interfaces

1 interface between chains.

A–B · 335 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5HT9 · Crystal structure of M-crystallin in the presence of nickel · 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 Q8TMX3
Elsewhere: RCSB PDB 5HT9 · PDBe 5HT9 · UniProt Q8TMX3

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