Research workbench
Elephant seal myoglobin esmb
Analyse Elephant seal myoglobin esmb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DDU
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myoglobin
- UniProt
- R9S002
- Ligands
- HEM, SO4
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Myoglobin | protein | 154 | 75% helix, 0% strand | R9S002 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 16 copies · chains A, C
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 | 192 | 0.69 | 0.86 | 30 | HEM |
| 2 | 189 | 0.68 | 0.86 | 31 | HEM |
| 3 | 160 | 0.59 | 0.82 | 19 | SO4 |
| 4 | 67 | 0.27 | 0.72 | 12 | SO4 |
Interfaces
1 interface between chains.
- A–C · 356 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7DDU · Elephant seal myoglobin esMb · 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 R9S002
- Elsewhere: RCSB PDB 7DDU · PDBe 7DDU · UniProt R9S002
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