MolNFT v1 · #165359 · protein

CD1 nitrite reductase nirs with bound dihydro-heme D1

6TSI: “CD1 nitrite reductase nirs with bound dihydro-heme D1”. X-ray diffraction, 4 ligands (HEC, DHE, PO4), 6 pockets (best druggability 0.85). MolNFT v1 #165359 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6TSI
Type: protein
Length: 1,080 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrite reductase
EC: 1.7.2.1, 1.7.99.1
UniProt: P24474
Ligands: HEC, DHE, PO4, CL
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrite reductase (EC 1.7.2.1, 1.7.99.1)	protein	540	16% helix, 38% strand	P24474

Ligands and binding sites

HEC · Heme C · ligand · 2 copies · chains A, B
DHE · Heme D · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 5 copies · chains A, B
CL · Chloride ion · ion · 5 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1004	0.85	0.86	114	HEC, DHE
2	1047	0.85	0.86	124	HEC, DHE, PO4
3	463	0.83	0.90	53	CL
4	996	0.78	0.80	69	empty
5	161	0.44	0.75	23	CL

Interfaces

1 interface between chains.

A–B · 3449 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (heme c attachment).

Compared structures

6TSI · cd1 nitrite reductase NirS with bound dihydro-heme d1 · the same entry in another collection · chain A against A, TM-score 1.00
P24474 · AlphaFold monomer V2.0 prediction for nitrite reductase (P24474) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 P24474
Elsewhere: RCSB PDB 6TSI · PDBe 6TSI · UniProt P24474

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.