Research workbench
Structure of malonyl-coenzyme a reductase from crenarchaeota in complex with CoA
Analyse Structure of malonyl-coenzyme a reductase from crenarchaeota in complex with CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DPM
- Type
- protein
- Length
- 2,122 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malonyl-COA/SUCCINYL-CoA reductase
- EC
- 1.2.1.75, 1.2.1.76
- UniProt
- Q96YK1
- Ligands
- COA, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malonyl-COA/SUCCINYL-CoA reductase (EC 1.2.1.75, 1.2.1.76) | protein | 354 | 34% helix, 22% strand | Q96YK1 |
| E, F | Malonyl-COA/SUCCINYL-CoA reductase (EC 1.2.1.75, 1.2.1.76) | protein | 353 | 33% helix, 23% strand | Q96YK1 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.98 | 28 | empty |
| 2 | 553 | 0.74 | 0.82 | 68 | empty |
| 3 | 687 | 0.73 | 0.79 | 76 | empty |
| 4 | 776 | 0.67 | 0.75 | 66 | empty |
| 5 | 298 | 0.63 | 0.80 | 43 | COA |
Interfaces
11 interfaces between chains.
- E–F · 1751 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1748 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 776 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 761 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 752 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4DPM · Structure of malonyl-coenzyme A reductase from crenarchaeota in complex with CoA · the same entry in another collection · chain F against F, TM-score 1.00
- Q96YK1 · AlphaFold monomer V2.0 prediction for malonyl-CoA reductase (Q96YK1) · a predicted model of the same protein · 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
- Every structure of UniProt Q96YK1
- Elsewhere: RCSB PDB 4DPM · PDBe 4DPM · UniProt Q96YK1
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