MolNFT v1 · #82412 · protein
Dimeric horse myoglobin
3VM9: “Dimeric horse myoglobin”. X-ray diffraction, 2 ligands (HEM, O), 4 pockets (best druggability 0.72). MolNFT v1 #82412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VM9
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myoglobin
- UniProt
- P68082
- Ligands
- HEM, O
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myoglobin | protein | 153 | 80% helix, 0% strand | P68082 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- O · Oxygen atom · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.72 | 0.88 | 25 | O, HEM |
| 2 | 191 | 0.72 | 0.88 | 26 | HEM, O |
| 3 | 162 | 0.45 | 0.76 | 23 | empty |
| 4 | 80 | 0.39 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2950 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3VM9 · Dimeric horse myoglobin · 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 P68082
- Elsewhere: RCSB PDB 3VM9 · PDBe 3VM9 · UniProt P68082
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.