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Nickel-bound C-terminal regulatory domain of nikr

Analyse Nickel-bound C-terminal regulatory domain of nikr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q5Y
Type: protein
Length: 329 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel responsive regulator
UniProt: P0A6Z6
Ligands: NI
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel responsive regulator	protein	84	33% helix, 46% strand	P0A6Z6
B	Nickel responsive regulator	protein	83	33% helix, 47% strand	P0A6Z6
C	Nickel responsive regulator	protein	82	34% helix, 45% strand	P0A6Z6
D	Nickel responsive regulator	protein	80	26% helix, 49% strand	P0A6Z6

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	106	0.79	0.98	24	empty
2	150	0.47	0.77	21	empty
3	77	0.44	0.80	15	empty
4	143	0.44	0.76	20	empty
5	77	0.42	0.79	16	empty

Interfaces

6 interfaces between chains.

A–C · 990 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 944 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 885 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 881 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 101 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1Q5Y · Nickel-Bound C-terminal Regulatory Domain of NikR · the same entry in another collection · chain C against C, TM-score 1.00
P0A6Z6 · AlphaFold monomer V2.0 prediction for nickel-responsive regulator (P0A6Z6) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P0A6Z6
Elsewhere: RCSB PDB 1Q5Y · PDBe 1Q5Y · UniProt P0A6Z6

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