Research workbench
X-ray crystal structure of tmpa, 2-trimethylaminoethylphosphonate hydroxylase, with fe and 2OG
Analyse X-ray crystal structure of tmpa, 2-trimethylaminoethylphosphonate hydroxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NPB
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tmpa, 2-trimethylaminoethylphosphonate hydroxylase
- EC
- 1.-.-.-
- Ligands
- AKG, FE2, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tmpa, 2-trimethylaminoethylphosphonate hydroxylase (EC 1.-.-.-) | protein | 377 | 26% helix, 32% strand | — |
| B | Tmpa, 2-trimethylaminoethylphosphonate hydroxylase (EC 1.-.-.-) | protein | 378 | 27% helix, 33% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.81 | 0.83 | 102 | SO4 |
| 2 | 93 | 0.77 | 0.98 | 26 | FE2, AKG, SO4 |
| 3 | 519 | 0.68 | 0.78 | 50 | FE2, SO4 |
| 4 | 163 | 0.52 | 0.79 | 31 | empty |
| 5 | 85 | 0.46 | 0.81 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 3740 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6NPB · X-ray crystal structure of TmpA, 2-trimethylaminoethylphosphonate hydroxylase, with Fe… · 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 6NPB · PDBe 6NPB
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