MolNFT v1 · #126178 · protein
2.12 a resolution structure of ptxb from prochlorococcus marinus (mit 9301) in complex with phosphite
5LV1: “2.12 a resolution structure of ptxb from prochlorococcus marinus (mit 9301) in complex with phosphite”. X-ray diffraction, 1 ligand (78T), 6 pockets (best druggability 0.69). MolNFT v1 #126178 on GenesisL1: 3D structure, binding…
- PDB
- 5LV1
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ptxb
- UniProt
- A3PDP9
- Ligands
- 78T
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Ptxb | protein | 264 | 42% helix, 24% strand | A3PDP9 |
Ligands and binding sites
- 78T · oxidanylphosphinate · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.69 | 0.83 | 31 | empty |
| 2 | 276 | 0.69 | 0.84 | 31 | empty |
| 3 | 304 | 0.68 | 0.83 | 33 | empty |
| 4 | 501 | 0.63 | 0.76 | 45 | empty |
| 5 | 88 | 0.34 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 391 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 161 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5LV1 · 2.12 A resolution structure of PtxB from Prochlorococcus marinus (MIT 9301) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- A3PDP9 · AlphaFold monomer V2.0 prediction for probable ABC transporter PHOSPHONATE/PHOSPHITE… · a predicted model of the same protein · 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 A3PDP9
- Elsewhere: RCSB PDB 5LV1 · PDBe 5LV1 · UniProt A3PDP9
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