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The structure of TRP repressor binding protein from bacillus subtilis
Analyse The structure of TRP repressor binding protein from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RLI
- Type
- protein
- Length
- 645 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRP repressor binding protein
- UniProt
- P96726
- Ligands
- PT, PO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRP repressor binding protein | protein | 156 | 44% helix, 22% strand | P96726 |
| B | TRP repressor binding protein | protein | 156 | 44% helix, 22% strand | P96726 |
| C | TRP repressor binding protein | protein | 165 | 39% helix, 24% strand | P96726 |
| D | TRP repressor binding protein | protein | 168 | 40% helix, 24% strand | P96726 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 11 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.75 | 0.84 | 50 | empty |
| 2 | 350 | 0.75 | 0.86 | 39 | empty |
| 3 | 427 | 0.70 | 0.81 | 49 | PT |
| 4 | 447 | 0.69 | 0.80 | 51 | PT |
| 5 | 188 | 0.56 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1248 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1207 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 905 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 164 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1RLI · The Structure of Trp Repressor Binding Protein from Bacillus subtilis · the same entry in another collection · chain D against D, TM-score 1.00
- P96726 · AlphaFold monomer V2.0 prediction for putative NAD(P)H-dependent FMN- containing… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P96726
- Elsewhere: RCSB PDB 1RLI · PDBe 1RLI · UniProt P96726
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