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Crystal structure of nitrophorin 1 from rhodnius prolixus

Analyse Crystal structure of nitrophorin 1 from rhodnius prolixus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NP1
Type: protein
Length: 368 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrophorin 1
UniProt: Q26239
Ligands: HEM, NH4, 2HP
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrophorin 1	protein	184	13% helix, 45% strand	Q26239

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NH4 · Ammonium ion · ion · 2 copies · chains A, B
2HP · Dihydrogenphosphate ion · ion · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.75	0.84	43	NH4, HEM
2	456	0.73	0.82	43	NH4, HEM
3	78	0.39	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 48 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2NP1 · Crystal structure of nitrophorin 1 from rhodnius prolixus · the same entry in another collection · chain A against A, TM-score 1.00
Q26239 · AlphaFold monomer V2.0 prediction for nitrophorin-1 (Q26239) · 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 Q26239
Elsewhere: RCSB PDB 2NP1 · PDBe 2NP1 · UniProt Q26239

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