Research workbench
Mpns crystallized in the absence of substrate
Analyse Mpns crystallized in the absence of substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B9S
- Type
- protein
- Length
- 3,472 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
- FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylphosphonate synthase (EC 1.13.11.73) | protein | 442 | 29% helix, 28% strand | A9A1T2 |
| D, E | Methylphosphonate synthase (EC 1.13.11.73) | protein | 441 | 30% helix, 28% strand | A9A1T2 |
| C | Methylphosphonate synthase (EC 1.13.11.73) | protein | 439 | 31% helix, 28% strand | A9A1T2 |
| F | Methylphosphonate synthase (EC 1.13.11.73) | protein | 397 | 24% helix, 31% strand | A9A1T2 |
| G | Methylphosphonate synthase (EC 1.13.11.73) | protein | 442 | 30% helix, 28% strand | A9A1T2 |
| B | Methylphosphonate synthase (EC 1.13.11.73) | protein | 441 | 30% helix, 27% strand | A9A1T2 |
| H | Methylphosphonate synthase (EC 1.13.11.73) | protein | 429 | 28% helix, 29% strand | A9A1T2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 5 copies · chains A, B, D, C, G, E
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 | 1093 | 0.88 | 0.89 | 122 | FE |
| 2 | 284 | 0.84 | 0.95 | 49 | empty |
| 3 | 760 | 0.83 | 0.87 | 69 | empty |
| 4 | 1009 | 0.83 | 0.84 | 89 | empty |
| 5 | 844 | 0.82 | 0.85 | 73 | empty |
Interfaces
10 interfaces between chains.
- A–B · 7580 Ų buried · 133 hydrogen bonds · protein-protein
- D–C · 7027 Ų buried · 124 hydrogen bonds · protein-protein
- G–H · 6826 Ų buried · 109 hydrogen bonds · protein-protein
- F–E · 6823 Ų buried · 114 hydrogen bonds · protein-protein
- C–F · 479 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 6B9S · PDBe 6B9S · UniProt A9A1T2
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