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Crystal structure of escherichia COLI nrfa with europium bound

Analyse Crystal structure of escherichia COLI nrfa with europium bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TOR
Type: protein
Length: 1,764 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C nitrite reductase
EC: 1.7.2.2
UniProt: P0ABK9
Ligands: HEC, EU, CA
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cytochrome C nitrite reductase (EC 1.7.2.2)	protein	441	57% helix, 5% strand	P0ABK9

Ligands and binding sites

HEC · Heme C · ligand · 20 copies · chains A, D, B, C
EU · Europium ion · metal · 9 copies · chains A, D, B, C
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	791	0.89	0.92	91	HEC
2	741	0.88	0.92	100	HEC
3	752	0.88	0.91	97	HEC
4	681	0.87	0.92	92	HEC
5	229	0.76	0.90	39	HEC, EU

Interfaces

4 interfaces between chains.

A–D · 1541 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1537 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 216 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 56 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 35 cofactor (heme c attachment).

Compared structures

3TOR · Crystal structure of Escherichia coli NrfA with Europium bound · 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 3TOR · PDBe 3TOR · UniProt P0ABK9

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