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Crystal structure of polyprenyl synthase PATL_3739 (target efi-509195) from pseudoalteromonas atlantica, complex with inorganic phosphate and an unknown ligand
Analyse Crystal structure of polyprenyl synthase PATL_3739 (target efi-509195) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JYX
- Type
- protein
- Length
- 2,511 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-hexaprenyltranstransferase
- EC
- 2.5.1.30
- UniProt
- Q15PE7
- Ligands
- UNL, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 317 | 74% helix, 1% strand | Q15PE7 |
| B | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 316 | 75% helix, 1% strand | Q15PE7 |
| C | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 311 | 77% helix, 0% strand | Q15PE7 |
| D | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 312 | 77% helix, 0% strand | Q15PE7 |
| E | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 310 | 77% helix, 0% strand | Q15PE7 |
| F | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 312 | 78% helix, 0% strand | Q15PE7 |
| H | Trans-hexaprenyltranstransferase (EC 2.5.1.30) | protein | 316 | 75% helix, 1% strand | Q15PE7 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, C, B, D, F, G, E, H
- PO4 · Phosphate ion · ion · 13 copies · chains A, B, C, D, E, F, G, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.75 | 0.99 | 17 | UNL |
| 2 | 1161 | 0.74 | 0.77 | 104 | empty |
| 3 | 66 | 0.74 | 0.98 | 16 | UNL |
| 4 | 63 | 0.74 | 0.99 | 17 | UNL |
| 5 | 627 | 0.73 | 0.80 | 53 | PO4 |
Interfaces
12 interfaces between chains.
- A–C · 2037 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2010 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 2004 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1976 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4JYX · Crystal structure of polyprenyl synthase PATL_3739 (TARGET EFI-509195) FROM… · 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 Q15PE7
- Elsewhere: RCSB PDB 4JYX · PDBe 4JYX · UniProt Q15PE7
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