Research workbench

NIKR-APO

Analyse NIKR-APO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BJ3
Type: protein
Length: 540 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel responsive regulator
UniProt: O58316
Ligands: MG, CL
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel responsive regulator	protein	135	42% helix, 36% strand	O58316
B	Nickel responsive regulator	protein	137	42% helix, 35% strand	O58316
C	Nickel responsive regulator	protein	138	42% helix, 35% strand	O58316
D	Nickel responsive regulator	protein	130	44% helix, 35% strand	O58316

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B, D
CL · Chloride ion · ion · 2 copies · chains B, C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	108	0.76	0.96	21	empty
2	300	0.59	0.78	25	empty
3	249	0.55	0.77	33	empty
4	258	0.55	0.77	25	empty
5	235	0.53	0.77	27	empty

Interfaces

6 interfaces between chains.

A–B · 3178 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 3132 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 851 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 744 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 114 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2BJ3 · NIKR-apo · the same entry in another collection · chain D against D, TM-score 1.00
O58316 · AlphaFold monomer V2.0 prediction for putative nickel-responsive regulator (O58316) · a predicted model of the same protein · chain A against A, TM-score 0.68

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 O58316
Elsewhere: RCSB PDB 2BJ3 · PDBe 2BJ3 · UniProt O58316

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