MolNFT v1 · #102887 · protein

GLNK2 from haloferax mediterranei complexed with ATP

4OZN · Nitrogen regulatory protein P-II: “GLNK2 from haloferax mediterranei complexed with ATP”. X-ray diffraction, 2 ligands (ATP, SO4), 3 pockets (best druggability 0.67). MolNFT v1 #102887 on GenesisL1: 3D structure, binding sites and…

PDB: 4OZN
Type: protein
Length: 333 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrogen regulatory protein P-II
UniProt: B8ZYW1
Ligands: ATP, SO4
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrogen regulatory protein P-II	protein	116	35% helix, 34% strand	B8ZYW1
B	Nitrogen regulatory protein P-II	protein	104	31% helix, 38% strand	B8ZYW1
C	Nitrogen regulatory protein P-II	protein	113	28% helix, 35% strand	B8ZYW1

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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

Pockets

3 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	301	0.67	0.82	39	ATP
2	249	0.67	0.84	36	ATP
3	189	0.65	0.85	27	ATP

Interfaces

3 interfaces between chains.

A–B · 1253 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 1219 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1187 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4OZN · GlnK2 from Haloferax mediterranei complexed with ATP · the same entry in another collection · chain B against B, TM-score 1.00
B8ZYW1 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein GLNK2 (B8ZYW1) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 B8ZYW1
Elsewhere: RCSB PDB 4OZN · PDBe 4OZN · UniProt B8ZYW1

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