Research workbench
Crystal structure of the M. tuberculosis phosphate ABC transport receptor psts-1 in complex with Fab P4-170
Analyse Crystal structure of the M. tuberculosis phosphate ABC transport receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DM2
- Type
- protein
- Length
- 762 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate-binding protein psts 1; Light chain; Heavy chain
- UniProt
- P9WGU1
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphate-binding protein psts 1 | protein | 334 | 37% helix, 20% strand | P9WGU1 |
| L | Light chain | protein | 211 | 8% helix, 52% strand | — |
| H | Heavy chain | protein | 217 | 7% helix, 50% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.69 | 0.91 | 31 | empty |
| 2 | 396 | 0.56 | 0.74 | 51 | empty |
| 3 | 169 | 0.50 | 0.77 | 32 | empty |
| 4 | 147 | 0.48 | 0.77 | 29 | empty |
| 5 | 89 | 0.37 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1699 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 538 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 520 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7DM2 · crystal structure of the M. tuberculosis phosphate ABC transport receptor PstS-1 in… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WGU1 · AlphaFold monomer V2.0 prediction for phosphate-binding protein psts 1 (P9WGU1) · 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 P9WGU1
- Elsewhere: RCSB PDB 7DM2 · PDBe 7DM2 · UniProt P9WGU1
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