MolNFT v1 · #28372 · protein
Distal pocket polarity in ligand binding to myoglobin: deoxy and carbonmonoxy forms of a THREONINE68 (E11) mutant investigated by X-ray crystallography and infrared spectroscopy
1YCA: “Distal pocket polarity in ligand binding to myoglobin: deoxy and carbonmonoxy forms of a THREONINE68 (E11)…”. X-ray diffraction, 2 ligands (HEM, CMO), 2 pockets (best druggability 0.70). MolNFT v1 #28372 on GenesisL1: 3D structure…
- PDB
- 1YCA
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myoglobin
- UniProt
- P02189
- Ligands
- HEM, CMO
- Pockets
- 2 · best druggability 0.70
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 | P02189 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CMO · Carbon monoxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.70 | 0.87 | 23 | HEM, CMO |
| 2 | 211 | 0.69 | 0.85 | 30 | HEM, CMO |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1YCA · Distal pocket polarity in ligand binding to myoglobin: deoxy and carbonmonoxy forms of a… · the same entry in another collection · chain A against A, TM-score 1.00
- P02189 · AlphaFold monomer V2.0 prediction for myoglobin (P02189) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P02189
- Elsewhere: RCSB PDB 1YCA · PDBe 1YCA · UniProt P02189
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.