Research workbench

Esherichia COLI nitrite reductase nrfa H264N

Analyse Esherichia COLI nitrite reductase nrfa H264N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WJY
Type: protein
Length: 882 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C-552
EC: 1.7.2.2
UniProt: P0ABK9
Ligands: HEC, CA
Pockets: 11 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytochrome C-552 (EC 1.7.2.2)	protein	441	58% helix, 5% strand	P0ABK9

Ligands and binding sites

HEC · Heme C · ligand · 10 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

11 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	830	0.88	0.91	112	HEC
2	832	0.88	0.91	109	HEC
3	172	0.72	0.89	33	HEC
4	68	0.60	0.90	16	HEC
5	147	0.56	0.82	25	empty

Interfaces

1 interface between chains.

A–B · 1556 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 cofactor (heme c attachment).

Compared structures

4WJY · Esherichia coli nitrite reductase NrfA H264N · the same entry in another collection · chain A against A, TM-score 1.00
P0ABK9 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P0ABK9) · 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 P0ABK9
Elsewhere: RCSB PDB 4WJY · PDBe 4WJY · UniProt P0ABK9

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