MolNFT v1 · #184998 · protein
Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, ggpp and ispp
7PB1 · Dehydrodolichyl diphosphate synthase complex subunit dhdds: “Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, ggpp and ispp”. X-ray diffraction, 3 ligands (GRG, ISY, MG), 5 pockets…
- PDB
- 7PB1
- Type
- protein
- Length
- 502 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
- GRG, ISY, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrodolichyl diphosphate synthase complex subunit dhdds (EC 2.5.1.87) | protein | 320 | 61% helix, 11% strand | Q86SQ9 |
| B | Dehydrodolichyl diphosphate synthase complex subunit NUS1 (EC 2.5.1.87) | protein | 182 | 48% helix, 14% strand | Q96E22 |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · chains A, B
- ISY · 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.80 | 0.86 | 60 | MG, GRG, ISY |
| 2 | 429 | 0.63 | 0.77 | 38 | empty |
| 3 | 174 | 0.46 | 0.76 | 30 | empty |
| 4 | 87 | 0.41 | 0.78 | 21 | empty |
| 5 | 75 | 0.36 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2027 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7PB1 · 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
- Q96E22 · AlphaFold monomer V2.0 prediction for dehydrodolichyl diphosphate synthase complex… · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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
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 7PB1 · PDBe 7PB1 · UniProt Q86SQ9 · UniProt Q96E22
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