Research workbench

1.08 a structure of ferrous NP4 (aquo complex)

Analyse 1.08 a structure of ferrous NP4 (aquo complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YWD
Type: protein
Length: 184 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrophorin 4
UniProt: Q94734
Ligands: HEM
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrophorin 4	protein	184	13% helix, 43% strand	Q94734

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	460	0.75	0.83	45	HEM

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1YWD · 1.08 A Structure of Ferrous NP4 (aquo complex) · the same entry in another collection · chain A against A, TM-score 1.00
Q94734 · AlphaFold monomer V2.0 prediction for nitrophorin-4 (Q94734) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q94734
Elsewhere: RCSB PDB 1YWD · PDBe 1YWD · UniProt Q94734

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