Research workbench
The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2B) bound to human dihydrolipoamide dehydrogenase (E3)
Analyse The crystal structure of the subunit binding of human dihydrolipoamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RNM
- Type
- protein
- Length
- 1,974 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase, mitochondrial; Lipoamide acyltransferase component of…
- EC
- 1.8.1.4, 2.3.1.168
- UniProt
- P09622, P11182
- Ligands
- FAD
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 472 | 35% helix, 27% strand | P09622 |
| B, D | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 468 | 35% helix, 26% strand | P09622 |
| E | Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial (EC 2.3.1.168) | protein | 51 | 61% helix, 0% strand | P11182 |
| F | Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial (EC 2.3.1.168) | protein | 43 | 63% helix, 0% strand | P11182 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.85 | 0.88 | 53 | empty |
| 2 | 764 | 0.84 | 0.87 | 65 | empty |
| 3 | 853 | 0.80 | 0.83 | 89 | BME, FAD |
| 4 | 917 | 0.80 | 0.82 | 99 | BME, FAD |
| 5 | 806 | 0.80 | 0.83 | 96 | BME, FAD |
Interfaces
8 interfaces between chains.
- A–B · 4125 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 4095 Ų buried · 61 hydrogen bonds · protein-protein
- A–E · 475 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 470 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 302 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (additive adduct, disulfide).
Compared structures
- 3RNM · The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b)… · the same entry in another collection · chain F against F, TM-score 1.00
- P09622 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase, mitochondrial (P09622) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P11182 · AlphaFold monomer V2.0 prediction for lipoamide acyltransferase component of… · a predicted model of the same protein · chain F against A, TM-score 0.94
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 P09622
- Every structure of UniProt P11182
- Elsewhere: RCSB PDB 3RNM · PDBe 3RNM · UniProt P09622 · UniProt P11182
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