Research workbench
Hmob structure with heme
Analyse Hmob structure with heme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FVC
- Type
- protein
- Length
- 901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein yhgc
- UniProt
- E0TXX3
- Ligands
- HEM
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative uncharacterized protein yhgc | protein | 149 | 21% helix, 42% strand | E0TXX3 |
| E | Putative uncharacterized protein yhgc | protein | 151 | 21% helix, 41% strand | E0TXX3 |
| F | Putative uncharacterized protein yhgc | protein | 154 | 20% helix, 41% strand | E0TXX3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.62 | 0.75 | 39 | empty |
| 2 | 205 | 0.56 | 0.79 | 26 | HEM |
| 3 | 207 | 0.56 | 0.79 | 24 | HEM |
| 4 | 191 | 0.56 | 0.79 | 24 | HEM |
| 5 | 178 | 0.55 | 0.79 | 22 | HEM |
Interfaces
6 interfaces between chains.
- C–F · 725 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 667 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 180 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 130 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FVC · HmoB structure with heme · 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 E0TXX3
- Elsewhere: RCSB PDB 4FVC · PDBe 4FVC · UniProt E0TXX3
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