MolNFT v1 · #17123 · protein
Human brain neuroglobin three-dimensional structure
1OJ6: “Human brain neuroglobin three-dimensional structure”. X-ray diffraction, 2 ligands (HEM, SO4), 6 pockets (best druggability 0.83). MolNFT v1 #17123 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OJ6
- Type
- protein
- Length
- 596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroglobin
- UniProt
- Q9NPG2
- Ligands
- HEM, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 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.
| Volume (ų) | 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 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 701 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 349 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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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