MolNFT v1 · #59011 · protein

Apo C-terminal domain of nikr

3BKU · Nickel-responsive regulator: “Apo C-terminal domain of nikr”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #59011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BKU
Type: protein
Length: 299 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel-responsive regulator
UniProt: P0A6Z6
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel-responsive regulator	protein	68	19% helix, 50% strand	P0A6Z6
B	Nickel-responsive regulator	protein	82	30% helix, 48% strand	P0A6Z6
C	Nickel-responsive regulator	protein	83	35% helix, 45% strand	P0A6Z6
D	Nickel-responsive regulator	protein	66	20% helix, 52% strand	P0A6Z6

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.67	0.96	15	empty
2	404	0.63	0.77	39	empty
3	309	0.60	0.78	46	empty
4	146	0.41	0.74	25	empty
5	97	0.36	0.74	18	empty

Interfaces

6 interfaces between chains.

C–D · 805 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 781 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 583 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 393 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 94 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3BKU · Apo C-terminal Domain of NikR · the same entry in another collection · chain D against D, 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 0.94

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 3BKU · PDBe 3BKU · UniProt P0A6Z6

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