Research workbench
Hmg-CoA reductase from methanothermococcus thermolithotrophicus in complex with NADPH at 2.9 a resolution
Analyse Hmg-CoA reductase from methanothermococcus thermolithotrophicus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HR8
- Type
- protein
- Length
- 2,377 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmg-CoA reductase
- EC
- 1.1.1.34
- Ligands
- NAP, NA, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hmg-CoA reductase (EC 1.1.1.34) | protein | 397 | 47% helix, 25% strand | — |
| B | Hmg-CoA reductase (EC 1.1.1.34) | protein | 396 | 47% helix, 26% strand | — |
| C, D, E, F | Hmg-CoA reductase (EC 1.1.1.34) | protein | 396 | 46% helix, 25% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 2 copies · chains D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.74 | 0.79 | 84 | PEG |
| 2 | 458 | 0.69 | 0.80 | 50 | empty |
| 3 | 455 | 0.68 | 0.80 | 51 | empty |
| 4 | 435 | 0.67 | 0.79 | 51 | empty |
| 5 | 226 | 0.65 | 0.83 | 32 | empty |
Interfaces
9 interfaces between chains.
- C–D · 5004 Ų buried · 103 hydrogen bonds · protein-protein
- A–B · 4980 Ų buried · 96 hydrogen bonds · protein-protein
- E–F · 4749 Ų buried · 89 hydrogen bonds · protein-protein
- B–D · 1367 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1345 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6HR8 · HMG-CoA reductase from Methanothermococcus thermolithotrophicus in complex with NADPH at… · 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
- Elsewhere: RCSB PDB 6HR8 · PDBe 6HR8
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