MolNFT v1 · #48317 · protein
Crystal structure of putative isomerase from sinorhizobium meliloti
2PPG: “Crystal structure of putative isomerase from sinorhizobium meliloti”. X-ray diffraction, 18 pockets (best druggability 0.86). MolNFT v1 #48317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2PPG
- Type
- protein
- Length
- 1,522 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative isomerase
- UniProt
- Q92ZS5
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative isomerase | protein | 387 | 42% helix, 22% strand | Q92ZS5 |
| B | Putative isomerase | protein | 370 | 42% helix, 24% strand | Q92ZS5 |
| C | Putative isomerase | protein | 382 | 40% helix, 22% strand | Q92ZS5 |
| D | Putative isomerase | protein | 383 | 39% helix, 21% strand | Q92ZS5 |
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.86 | 0.88 | 107 | empty |
| 2 | 383 | 0.86 | 0.94 | 41 | empty |
| 3 | 384 | 0.85 | 0.94 | 41 | empty |
| 4 | 594 | 0.78 | 0.84 | 63 | empty |
| 5 | 271 | 0.74 | 0.88 | 49 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2294 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1072 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1060 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 476 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 459 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 2PPG · Crystal structure of putative isomerase from Sinorhizobium meliloti · 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 Q92ZS5
- Elsewhere: RCSB PDB 2PPG · PDBe 2PPG · UniProt Q92ZS5
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