Research workbench
Heterodimeric myoglobin formed by domain swapping
Analyse Heterodimeric myoglobin formed by domain swapping in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WYO
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myoglobin
- UniProt
- P68082
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Myoglobin | protein | 153 | 78% helix, 0% strand | P68082 |
| B, D | Myoglobin | protein | 153 | 78% helix, 0% strand | P68082 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.81 | 0.82 | 86 | HEM |
| 2 | 220 | 0.73 | 0.88 | 31 | HEM |
| 3 | 224 | 0.72 | 0.87 | 32 | HEM |
| 4 | 232 | 0.72 | 0.86 | 32 | HEM |
| 5 | 690 | 0.69 | 0.77 | 68 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2766 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2743 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3WYO · Heterodimeric myoglobin formed by domain swapping · 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 3WYO · PDBe 3WYO · UniProt P68082
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