Research workbench
X-ray crystal structure of tmpb, (R)-1-hydroxy-2- trimethylaminoethylphosphonate oxygenase, with (R)-1-hydroxy-2- trimethylaminoethylphosphonate
Analyse X-ray crystal structure of tmpb, (R)-1-hydroxy-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NPA
- Type
- protein
- Length
- 737 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tmpb, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase
- EC
- 1.-.-.-
- Ligands
- KVP, FE, FE2
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tmpb, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase (EC 1.-.-.-) | protein | 188 | 66% helix, 1% strand | — |
| B | Tmpb, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase (EC 1.-.-.-) | protein | 187 | 66% helix, 1% strand | — |
| C, D | Tmpb, (R)-1-hydroxy-2-trimethylaminoethylphosphonate oxygenase (EC 1.-.-.-) | protein | 181 | 65% helix, 1% strand | — |
Ligands and binding sites
- KVP · (2R)-2-hydroxy-N,N,N-trimethyl-2-phosphonoethan-1-aminium · ligand · 2 copies · chains C, D
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.75 | 0.78 | 98 | FE2 |
| 2 | 866 | 0.68 | 0.75 | 67 | empty |
| 3 | 144 | 0.53 | 0.80 | 24 | FE2 |
| 4 | 94 | 0.45 | 0.80 | 25 | FE2, KVP |
| 5 | 77 | 0.44 | 0.81 | 20 | FE2, KVP |
Interfaces
4 interfaces between chains.
- A–B · 557 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 529 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 122 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NPA · X-ray crystal structure of TmpB, (R)-1-hydroxy-2-trimethylaminoethylphosphonate… · 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 6NPA · PDBe 6NPA
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