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Human brain neuroglobin three-dimensional structure

Analyse Human brain neuroglobin three-dimensional structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OJ6
Type: protein
Length: 596 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.95
Source: Homo sapiens
Molecule: Neuroglobin
UniProt: Q9NPG2
Ligands: HEM, SO4
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · resolution 1.95 · 4 distinct chains · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuroglobin	protein	147	78% helix, 0% strand	Q9NPG2
B	Neuroglobin	protein	151	74% helix, 1% strand	Q9NPG2
C	Neuroglobin	protein	148	77% helix, 1% strand	Q9NPG2
D	Neuroglobin	protein	150	77% helix, 0% strand	Q9NPG2

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 7 copies · chains B, A, C

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

Pockets

6 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	1025	0.83	0.84	111	empty
2	690	0.80	0.84	58	HEM, SO4
3	637	0.76	0.81	52	HEM, SO4
4	272	0.75	0.87	33	HEM
5	226	0.72	0.87	30	HEM

Interfaces

5 interfaces between chains.

A–D · 714 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 701 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 349 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 308 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 95 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1OJ6 · Human brain neuroglobin three-dimensional structure · the same entry in another collection · chain D against D, TM-score 1.00
Q9NPG2 · AlphaFold monomer V2.0 prediction for neuroglobin (Q9NPG2) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q9NPG2
Elsewhere: RCSB PDB 1OJ6 · PDBe 1OJ6 · UniProt Q9NPG2

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