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E. COLI nikr soaked with excess nickel ions

Analyse E. COLI nikr soaked with excess nickel ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OD2
Type: protein
Length: 261 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel-responsive regulatory protein
UniProt: C3SP37
Ligands: 3CM, NI
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel-responsive regulatory protein	protein	132	40% helix, 33% strand	C3SP37
B	Nickel-responsive regulatory protein	protein	129	39% helix, 36% strand	C3SP37

Ligands and binding sites

3CM · 3-cyclohexylpropyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · chains A, B
NI · Nickel (II) ion · metal · 11 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.52	0.76	25	empty

Interfaces

1 interface between chains.

A–B · 2356 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

3OD2 · E. coli NikR soaked with excess nickel ions · 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 C3SP37
Elsewhere: RCSB PDB 3OD2 · PDBe 3OD2 · UniProt C3SP37

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