Research workbench
Crystal structure of mpns with substrate 2-hydroxyethylphosphonate (2- hep) and FE(II) bound
Analyse Crystal structure of mpns 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
- 6B9T
- Type
- protein
- Length
- 3,572 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylphosphonate synthase
- EC
- 1.13.11.73
- UniProt
- A9A1T2
- Ligands
- 2HE, FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Methylphosphonate synthase (EC 1.13.11.73) | protein | 447 | 29% helix, 28% strand | A9A1T2 |
| B, G | Methylphosphonate synthase (EC 1.13.11.73) | protein | 446 | 29% helix, 28% strand | A9A1T2 |
| D | Methylphosphonate synthase (EC 1.13.11.73) | protein | 453 | 29% helix, 27% strand | A9A1T2 |
| E | Methylphosphonate synthase (EC 1.13.11.73) | protein | 444 | 30% helix, 28% strand | A9A1T2 |
| H | Methylphosphonate synthase (EC 1.13.11.73) | protein | 442 | 29% helix, 28% strand | A9A1T2 |
Ligands and binding sites
- 2HE · (2-hydroxyethyl)phosphonic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FE · Fe (III) ion · metal · 9 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.84 | 0.96 | 42 | empty |
| 2 | 270 | 0.84 | 0.96 | 45 | empty |
| 3 | 234 | 0.84 | 0.97 | 43 | empty |
| 4 | 279 | 0.84 | 0.95 | 43 | empty |
| 5 | 255 | 0.84 | 0.96 | 43 | empty |
Interfaces
13 interfaces between chains.
- C–D · 8288 Ų buried · 145 hydrogen bonds · protein-protein
- A–B · 8272 Ų buried · 147 hydrogen bonds · protein-protein
- E–F · 8125 Ų buried · 138 hydrogen bonds · protein-protein
- G–H · 8031 Ų buried · 129 hydrogen bonds · protein-protein
- A–H · 350 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6B9T · Crystal structure of MPnS with substrate 2-hydroxyethylphosphonate (2-HEP) and Fe(II)… · the same entry in another collection · chain H against H, TM-score 1.00
- A9A1T2 · AlphaFold monomer V2.0 prediction for methylphosphonate synthase (A9A1T2) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A9A1T2
- Elsewhere: RCSB PDB 6B9T · PDBe 6B9T · UniProt A9A1T2
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