MolNFT v1 · #90900 · protein
Crystal structure of phosphate ABC transporter, periplasmic phosphate- binding protein psts 1 (PBP1) from streptococcus pneumoniae canada MDR_19A
4EXL · Phosphate-binding protein psts 1: “Crystal structure of phosphate ABC transporter, periplasmic phosphate- binding protein psts 1 (PBP1) from…”. X-ray diffraction, 2 ligands (MG, CL), 10 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 4EXL
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate-binding protein psts 1
- UniProt
- Q97Q31
- Ligands
- MG, CL
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphate-binding protein psts 1 | protein | 261 | 36% helix, 27% strand | Q97Q31 |
| B | Phosphate-binding protein psts 1 | protein | 262 | 37% helix, 27% strand | Q97Q31 |
| C | Phosphate-binding protein psts 1 | protein | 262 | 36% helix, 26% strand | Q97Q31 |
| D | Phosphate-binding protein psts 1 | protein | 259 | 37% helix, 27% strand | Q97Q31 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, D, B, C
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.73 | 0.76 | 126 | empty |
| 2 | 1079 | 0.69 | 0.74 | 79 | empty |
| 3 | 294 | 0.66 | 0.82 | 44 | CL |
| 4 | 389 | 0.65 | 0.79 | 46 | empty |
| 5 | 56 | 0.60 | 0.92 | 17 | CL |
Interfaces
5 interfaces between chains.
- A–D · 576 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 360 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 244 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 216 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4EXL · Crystal structure of phosphate ABC transporter, periplasmic phosphate-binding protein… · the same entry in another collection · chain D against D, TM-score 1.00
- Q97Q31 · AlphaFold monomer V2.0 prediction for phosphate-binding protein psts 1 (Q97Q31) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q97Q31
- Elsewhere: RCSB PDB 4EXL · PDBe 4EXL · UniProt Q97Q31
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