Research workbench
1.41 a resolution structure of ptxb from trichodesmium erythraeum IMS101 in complex with methylphosphonate
Analyse 1.41 a resolution structure of ptxb from trichodesmium erythraeum IMS101 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LQ1
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonate ABC transporter, periplasmic phosphonate- binding protein
- UniProt
- Q119I9
- Ligands
- GB, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphonate ABC transporter, periplasmic phosphonate- binding protein | protein | 260 | 39% helix, 24% strand | Q119I9 |
| B | Phosphonate ABC transporter, periplasmic phosphonate- binding protein | protein | 256 | 42% helix, 25% strand | Q119I9 |
Ligands and binding sites
- GB · Methylphosphonic acid ester group · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.71 | 0.93 | 24 | empty |
| 2 | 118 | 0.71 | 0.92 | 25 | empty |
| 3 | 203 | 0.55 | 0.79 | 31 | empty |
| 4 | 243 | 0.54 | 0.76 | 22 | empty |
| 5 | 78 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 831 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5LQ1 · 1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with… · 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
- Every structure of UniProt Q119I9
- Elsewhere: RCSB PDB 5LQ1 · PDBe 5LQ1 · UniProt Q119I9
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