MolNFT v1 · #92944 · protein

Crystal structure of nitrophorin 4 triple mutant complex with ammonia

4GNW · Nitrophorin-4: “Crystal structure of nitrophorin 4 triple mutant complex with ammonia”. X-ray diffraction, 3 ligands (HEM, NH3, PO4), 5 pockets (best druggability 0.77). MolNFT v1 #92944 on GenesisL1: 3D structure, binding sites and…

PDB: 4GNW
Type: protein
Length: 368 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrophorin-4
UniProt: Q94734
Ligands: HEM, NH3, PO4
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrophorin-4	protein	184	17% helix, 45% strand	Q94734

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NH3 · Ammonia · ion · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

5 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	93	0.77	0.99	27	empty
2	319	0.77	0.87	38	HEM, NH3
3	325	0.76	0.87	37	HEM, NH3
4	139	0.56	0.82	31	empty
5	74	0.31	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 866 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4GNW · Crystal structure of nitrophorin 4 triple mutant complex with ammonia · 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 0.99

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 4GNW · PDBe 4GNW · UniProt Q94734

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