MolNFT v1 · #122719 · protein

Crystal structure of C139A nostoc H-nox domain with imidazole

5IXR · ALR2278 protein: “Crystal structure of C139A nostoc H-nox domain with imidazole”. X-ray diffraction, 1 ligand (HEM), 7 pockets (best druggability 0.84). MolNFT v1 #122719 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IXR
Type: protein
Length: 364 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ALR2278 protein
UniProt: Q8YUQ7
Ligands: HEM
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ALR2278 protein	protein	182	53% helix, 16% strand	Q8YUQ7

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
IMD · Imidazole · additive · 2 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.84	0.93	38	HEM, IMD
2	331	0.83	0.92	36	HEM, IMD
3	200	0.60	0.81	37	MLI
4	189	0.58	0.81	24	MLI
5	102	0.57	0.85	27	empty

Interfaces

1 interface between chains.

A–B · 984 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5IXR · Crystal Structure of C139A nostoc H-NOX domain with imidazole · the same entry in another collection · 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 Q8YUQ7
Elsewhere: RCSB PDB 5IXR · PDBe 5IXR · UniProt Q8YUQ7

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