Research workbench
Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, fspp and ipp
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
- 7PAX
- Type
- protein
- Length
- 528 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
- IPE, FPS, MG
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrodolichyl diphosphate synthase complex subunit dhdds (EC 2.5.1.87) | protein | 327 | 58% helix, 12% strand | Q86SQ9 |
| B | Dehydrodolichyl diphosphate synthase complex subunit NUS1 (EC 2.5.1.87) | protein | 201 | 50% helix, 13% strand | Q96E22 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A, B
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.84 | 0.94 | 41 | IPE, FPS, MG |
| 2 | 460 | 0.66 | 0.78 | 33 | empty |
| 3 | 127 | 0.58 | 0.84 | 26 | empty |
| 4 | 294 | 0.52 | 0.74 | 38 | empty |
| 5 | 71 | 0.42 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2095 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7PAX · 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 0.99
- Q96E22 · AlphaFold monomer V2.0 prediction for dehydrodolichyl diphosphate synthase complex… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 7PAX · PDBe 7PAX · UniProt Q86SQ9 · UniProt Q96E22
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