MolNFT v1 · #136257 · protein
The crystal structure of phosphoenolpyruvate phosphomutase from streptomyces platensis subsp. rosaceus
5UNC: “The crystal structure of phosphoenolpyruvate phosphomutase from streptomyces platensis subsp. rosaceus”. X-ray diffraction, 1 ligand (XYS), 15 pockets (best druggability 0.82). MolNFT v1 #136257 on GenesisL1: 3D structure, binding…
- PDB
- 5UNC
- Type
- protein
- Length
- 1,151 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate phosphomutase
- UniProt
- A0A0A0V023
- Ligands
- XYS
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate phosphomutase | protein | 289 | 49% helix, 12% strand | A0A0A0V023 |
| B, D | Phosphoenolpyruvate phosphomutase | protein | 287 | 51% helix, 13% strand | A0A0A0V023 |
| C | Phosphoenolpyruvate phosphomutase | protein | 288 | 49% helix, 13% strand | A0A0A0V023 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · 4 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · 5 copies · chains A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.82 | 0.97 | 30 | XYS |
| 2 | 156 | 0.81 | 0.97 | 29 | XYS |
| 3 | 853 | 0.81 | 0.83 | 95 | empty |
| 4 | 64 | 0.73 | 0.97 | 19 | empty |
| 5 | 62 | 0.73 | 0.98 | 21 | TLA |
Interfaces
6 interfaces between chains.
- A–B · 3141 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3053 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 949 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 931 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 653 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 5UNC · The crystal structure of PHOSPHOENOLPYRUVATE PHOSPHOMUTASE from Streptomyces platensis… · 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 A0A0A0V023
- Elsewhere: RCSB PDB 5UNC · PDBe 5UNC · UniProt A0A0A0V023
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