Research workbench
Crystal structure of the M.TUBERCULOSIS phosphate ABC transport receptor psts-1 in complex with Fab P4-36
Analyse Crystal structure of the M.TUBERCULOSIS phosphate ABC transport receptor psts-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DM1
- Type
- protein
- Length
- 1,534 residues
- Chains
- 6
- 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
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Phosphate-binding protein psts 1 | protein | 334 | 37% helix, 20% strand | P9WGU1 |
| C, E | Light chain | protein | 212 | 6% helix, 50% strand | — |
| D, F | Heavy chain | protein | 221 | 10% helix, 48% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.69 | 0.75 | 94 | empty |
| 2 | 618 | 0.68 | 0.77 | 69 | empty |
| 3 | 381 | 0.55 | 0.74 | 52 | empty |
| 4 | 347 | 0.52 | 0.73 | 47 | empty |
| 5 | 177 | 0.44 | 0.74 | 29 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1740 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1695 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 510 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 410 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 408 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7DM1 · crystal structure of the M.tuberculosis phosphate ABC transport receptor PstS-1 in… · the same entry in another collection · chain C against C, 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 B 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 7DM1 · PDBe 7DM1 · UniProt P9WGU1
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