MolNFT v1 · #56613 · protein
Crystal structure of hypothetical TRP repressor binding protein from sul folobus tokodaii (ST0872)
2ZKI · 199AA long hypothetical TRP repressor binding protein: “Crystal structure of hypothetical TRP repressor binding protein from sul folobus tokodaii (ST0872)”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.82).…
- PDB
- 2ZKI
- Type
- protein
- Length
- 1,555 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 199AA long hypothetical TRP repressor binding protein
- UniProt
- Q973M9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 199AA long hypothetical TRP repressor binding protein | protein | 196 | 41% helix, 17% strand | Q973M9 |
| B, C, F, H | 199AA long hypothetical TRP repressor binding protein | protein | 195 | 37% helix, 15% strand | Q973M9 |
| D | 199AA long hypothetical TRP repressor binding protein | protein | 194 | 41% helix, 15% strand | Q973M9 |
| E | 199AA long hypothetical TRP repressor binding protein | protein | 196 | 40% helix, 18% strand | Q973M9 |
| G | 199AA long hypothetical TRP repressor binding protein | protein | 189 | 40% helix, 19% strand | Q973M9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 49 copies · chains A, B, G, C, F, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.82 | 0.83 | 70 | SO4 |
| 2 | 470 | 0.66 | 0.78 | 36 | SO4 |
| 3 | 532 | 0.65 | 0.77 | 40 | SO4 |
| 4 | 414 | 0.64 | 0.78 | 35 | SO4 |
| 5 | 580 | 0.60 | 0.73 | 54 | SO4 |
Interfaces
15 interfaces between chains.
- A–B · 1408 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1322 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1319 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1286 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1279 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2ZKI · Crystal structure of hypothetical Trp repressor binding protein from Sul folobus tokodaii… · the same entry in another collection · 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 Q973M9
- Elsewhere: RCSB PDB 2ZKI · PDBe 2ZKI · UniProt Q973M9
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