Research workbench
Streptomyces albus hepd with substrate 2-hydroxyethylphosphonate (2- hep) and FE(II) bound
Analyse Streptomyces albus hepd with substrate 2-hydroxyethylphosphonate (2- hep) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B9R
- Type
- protein
- Length
- 1,772 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyethylphosphonate dioxygenase
- Ligands
- 2HE, FE
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Hydroxyethylphosphonate dioxygenase | protein | 442 | 29% helix, 27% strand | — |
| C | Hydroxyethylphosphonate dioxygenase | protein | 446 | 29% helix, 27% strand | — |
Ligands and binding sites
- 2HE · (2-hydroxyethyl)phosphonic acid · ligand · 4 copies · chains A, D, B, C
- FE · Fe (III) ion · metal · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.91 | 0.94 | 128 | empty |
| 2 | 785 | 0.91 | 0.95 | 121 | empty |
| 3 | 897 | 0.82 | 0.84 | 116 | GOL |
| 4 | 127 | 0.76 | 0.95 | 33 | empty |
| 5 | 92 | 0.75 | 0.96 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 7220 Ų buried · 117 hydrogen bonds · protein-protein
- B–C · 7117 Ų buried · 103 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 436 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6B9R · Streptomyces albus HEPD with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II) bound · 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 6B9R · PDBe 6B9R
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