MolNFT v1 · #77730 · protein
The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2B) bound to human dihydrolipoamide dehydrogenase (E3)
3RNM · Dihydrolipoyl dehydrogenase, mitochondrial: “The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2B) bound to human…”. X-ray diffraction, 1 ligand (FAD), 17 pockets (best druggability 0.85). MolNFT…
- 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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