Research workbench

Nitrite complex of tvnir, high dose data set (no complex)

Analyse Nitrite complex of tvnir, high dose data set (no complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4L3Y
Type: protein
Length: 1,040 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eight-heme nitrite reductase
EC: 1.7.2.2
UniProt: L0DSL2
Ligands: HEC, CA, NO2, SO4
Pockets: 9 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Eight-heme nitrite reductase (EC 1.7.2.2)	protein	520	45% helix, 10% strand	L0DSL2

Ligands and binding sites

HEC · Heme C · ligand · 16 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B
NO2 · Nitrite ion · ion · 6 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	820	0.88	0.91	95	HEC, NO2, CA
2	436	0.85	0.93	88	HEC
3	393	0.83	0.91	47	HEC
4	266	0.81	0.93	43	HEC, NO2
5	252	0.56	0.77	27	empty

Interfaces

1 interface between chains.

A–B · 1288 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 cofactor (heme c attachment).

Compared structures

4L3Y · Nitrite complex of TvNiR, high dose data set (NO complex) · the same entry in another collection · chain A against A, TM-score 1.00
L0DSL2 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (L0DSL2) · a predicted model of the same protein · 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 L0DSL2
Elsewhere: RCSB PDB 4L3Y · PDBe 4L3Y · UniProt L0DSL2

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