Research workbench
Hmgcr-UBIAD1 complex state 2
Analyse Hmgcr-UBIAD1 complex state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DJK
- Type
- protein
- Length
- 870 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxy-3-methylglutaryl-coenzyme a reductase; Ubia prenyltransferase domain-containing…
- EC
- 1.1.1.34
- UniProt
- P00347, G3IEF0, P0ABE7
- Ligands
- Y01, AJP
- Pockets
- 9 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.34) | protein | 245 | 82% helix, 0% strand | P00347 |
| B | Ubia prenyltransferase domain-containing protein 1 | protein | 281 | 78% helix, 0% strand | G3IEF0 |
| C | Soluble cytochrome B562 | protein | 120 | 82% helix, 0% strand | P0ABE7 |
| L | Fab 15B2 light chain | protein | 106 | 0% helix, 42% strand | — |
| H | Fab 15B2 heavy chain | protein | 118 | 5% helix, 43% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 6 copies · chains A, H, B
- AJP · Digitonin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.76 | 0.93 | 27 | empty |
| 2 | 1177 | 0.72 | 0.76 | 95 | AJP |
| 3 | 72 | 0.69 | 0.95 | 22 | empty |
| 4 | 385 | 0.67 | 0.80 | 47 | empty |
| 5 | 124 | 0.48 | 0.78 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1056 Ų buried · 4 hydrogen bonds · protein-protein
- L–H · 903 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 813 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 580 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 284 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 8DJK · HMGCR-UBIAD1 Complex State 2 · the same entry in another collection · chain B against B, TM-score 1.00
- P00347 · AlphaFold monomer V2.0 prediction for 3-hydroxy-3-methylglutaryl- coenzyme a reductase… · a predicted model of the same protein · chain A against A, TM-score 0.86
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 P00347
- Every structure of UniProt G3IEF0
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 8DJK · PDBe 8DJK · UniProt P00347 · UniProt G3IEF0 · UniProt P0ABE7
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