Research workbench
Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, ggspp and ispp
Analyse Structure of the human heterotetrameric cis-prenyltransferase complex in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PB0
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrodolichyl diphosphate synthase complex subunit dhdds; Dehydrodolichyl diphosphate…
- EC
- 2.5.1.87
- UniProt
- Q86SQ9, Q96E22
- Ligands
- ISY, GGS, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrodolichyl diphosphate synthase complex subunit dhdds (EC 2.5.1.87) | protein | 321 | 58% helix, 11% strand | Q86SQ9 |
| B | Dehydrodolichyl diphosphate synthase complex subunit NUS1 (EC 2.5.1.87) | protein | 200 | 48% helix, 13% strand | Q96E22 |
Ligands and binding sites
- ISY · 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid · ligand · chains A, B
- GGS · Phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6, 10,14-tetraenyl]sulfanyl-phosphinic acid · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.83 | 0.87 | 70 | ISY, GGS, MG |
| 2 | 452 | 0.65 | 0.78 | 36 | empty |
| 3 | 249 | 0.51 | 0.75 | 38 | empty |
| 4 | 85 | 0.41 | 0.79 | 18 | empty |
| 5 | 85 | 0.40 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2048 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7PB0 · Structure of the human heterotetrameric cis-prenyltransferase complex in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86SQ9 · AlphaFold monomer V2.0 prediction for dehydrodolichyl diphosphate synthase complex… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q96E22 · AlphaFold monomer V2.0 prediction for dehydrodolichyl diphosphate synthase complex… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q86SQ9
- Every structure of UniProt Q96E22
- Elsewhere: RCSB PDB 7PB0 · PDBe 7PB0 · UniProt Q86SQ9 · UniProt Q96E22
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