MolNFT v1 · #18978 · protein

APO-NIKR

1Q5V · Nickel responsive regulator: “APO-NIKR”. X-ray diffraction, 8 pockets (best druggability 0.65). MolNFT v1 #18978 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Q5V
Type: protein
Length: 476 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nickel responsive regulator
UniProt: P0A6Z6
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nickel responsive regulator	protein	115	38% helix, 38% strand	P0A6Z6
B	Nickel responsive regulator	protein	116	34% helix, 38% strand	P0A6Z6
C	Nickel responsive regulator	protein	115	36% helix, 38% strand	P0A6Z6
D	Nickel responsive regulator	protein	130	40% helix, 35% strand	P0A6Z6

Pockets

8 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	486	0.65	0.77	59	empty
2	430	0.61	0.76	39	empty
3	258	0.51	0.75	30	empty
4	126	0.39	0.74	23	empty
5	58	0.38	0.79	15	empty

Interfaces

6 interfaces between chains.

A–B · 2683 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 2608 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 481 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 395 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 90 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1Q5V · Apo-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 A against A, TM-score 0.84

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 1Q5V · PDBe 1Q5V · UniProt P0A6Z6

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