MolNFT v1 · #28990 · protein

Mixed valant state of nigerythrin

1YUX: “Mixed valant state of nigerythrin”. X-ray diffraction, 2 ligands (FE, FE2), 3 pockets (best druggability 0.63). MolNFT v1 #28990 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YUX
Type: protein
Length: 402 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nigerythrin
UniProt: P30820
Ligands: FE, FE2
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nigerythrin	protein	200	58% helix, 5% strand	P30820
B	Nigerythrin	protein	202	56% helix, 5% strand	P30820

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains A, B
FE2 · Fe (II) ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	414	0.63	0.78	61	empty
2	152	0.41	0.74	30	empty
3	54	0.26	0.73	11	empty

Interfaces

1 interface between chains.

A–B · 1521 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

1YUX · Mixed valant state of nigerythrin · the same entry in another collection · chain A against A, TM-score 1.00
P30820 · AlphaFold monomer V2.0 prediction for nigerythrin (P30820) · a predicted model of the same protein · chain B 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 P30820
Elsewhere: RCSB PDB 1YUX · PDBe 1YUX · UniProt P30820

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