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Copper-bound C-terminal domain of nikr

Analyse Copper-bound C-terminal 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: 3BKT
Type: protein
Length: 327 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel-responsive regulator
UniProt: P0A6Z6
Ligands: CU
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nickel-responsive regulator	protein	83	30% helix, 47% strand	P0A6Z6
C	Nickel-responsive regulator	protein	82	34% helix, 45% strand	P0A6Z6
D	Nickel-responsive regulator	protein	79	27% helix, 51% strand	P0A6Z6

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, C, B, 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	103	0.78	0.98	24	empty
2	184	0.49	0.76	23	empty
3	131	0.44	0.77	19	empty
4	67	0.42	0.80	16	empty
5	77	0.40	0.78	15	empty

Interfaces

6 interfaces between chains.

A–C · 988 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 975 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 886 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 821 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 102 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3BKT · Copper-bound C-terminal Domain of NikR · the same entry in another collection · chain A against A, TM-score 1.00
P0A6Z6 · AlphaFold monomer V2.0 prediction for nickel-responsive regulator (P0A6Z6) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 3BKT · PDBe 3BKT · UniProt P0A6Z6

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