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Structure of nitrite reductase ania from neisseria gonorrhoeae, space group I4122

Analyse Structure of nitrite reductase ania from neisseria gonorrhoeae, space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UE6
Type: protein
Length: 2,795 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrite reductase
UniProt: Q5F7A4
Ligands: CU, NA
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Nitrite reductase	protein	314	10% helix, 45% strand	Q5F7A4
B, C, E, H	Nitrite reductase	protein	310	9% helix, 45% strand	Q5F7A4
D	Nitrite reductase	protein	309	9% helix, 45% strand	Q5F7A4
F	Nitrite reductase	protein	307	9% helix, 45% strand	Q5F7A4
I	Nitrite reductase	protein	311	10% helix, 45% strand	Q5F7A4

Ligands and binding sites

CU · Copper (II) ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I
NA · Sodium ion · metal · 9 copies · chains A, C, B, D, F, E, G, I, H

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.87	0.88	118	CU
2	261	0.84	0.95	34	empty
3	250	0.83	0.95	37	empty
4	251	0.83	0.95	35	empty
5	57	0.70	0.97	17	empty

Interfaces

13 interfaces between chains.

H–I · 2259 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2164 Å² buried · 47 hydrogen bonds · protein-protein
G–H · 2156 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 2150 Å² buried · 47 hydrogen bonds · protein-protein
D–F · 2140 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

5UE6 · Structure of nitrite reductase AniA from Neisseria gonorrhoeae, space group I4122 · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5F7A4
Elsewhere: RCSB PDB 5UE6 · PDBe 5UE6 · UniProt Q5F7A4

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