Research workbench
Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) imidazole-ligand
Analyse Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) imidazole-ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YCJ
- Type
- protein
- Length
- 311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.58
- Source
- Physeter catodon
- Molecule
- Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly)
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.58 · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) | protein | 154 | 75% helix, 0% strand | — |
| B | Ancestral myoglobin aMbWb' of Basilosaurus relative (polyphyly) | protein | 157 | 75% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.69 | 0.80 | 48 | empty |
| 2 | 209 | 0.68 | 0.85 | 24 | HEM, IMD |
| 3 | 211 | 0.67 | 0.84 | 25 | HEM, IMD |
| 4 | 97 | 0.35 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 734 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5YCJ · Ancestral myoglobin ambwb' of basilosaurus relative (polyphyly) imidazole-ligand · 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
- Elsewhere: RCSB PDB 5YCJ · PDBe 5YCJ
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