MolNFT v2 · #205858 · protein + RNA
Structure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile
8CBO · 3-hydroxyacyl-CoA dehydrogenase type-2: “Structure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile”. Electron microscopy at 3.2, 2 ligands (NAD, SAH), 14 pockets (best druggability 0.86). MolNFT v2…
- PDB
- 8CBO
- Type
- protein + RNA
- Length
- 1,289 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- 3-hydroxyacyl-CoA dehydrogenase type-2; tRNA methyltransferase 10 homolog C…
- EC
- 1.1.1.35, 1.1.1.62, 1.1.1.239, 1.1.1.178, 1.1.1.53, 1.1.1.159, 2.1.1.-, 2.1.1.218, 2.1.1.221
- UniProt
- Q99714, Q7L0Y3
- Ligands
- NAD, SAH
- Pockets
- 14 · best druggability 0.86
Structure
electron microscopy · resolution 3.2 · 3 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-hydroxyacyl-CoA dehydrogenase type-2 (EC 1.1.1.35, 1.1.1.62, 1.1.1.239, 1.1.1.178, 1.1.1.53, 1.1.1.159) | protein | 255 | 45% helix, 15% strand | Q99714 |
| E | tRNA methyltransferase 10 homolog C (EC 2.1.1.-, 2.1.1.218, 2.1.1.221) | protein | 211 | 44% helix, 13% strand | Q7L0Y3 |
| T | Mitochondrial Precursor tRNA-Ile(5,4) | rna | 58 | — | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SAH · S-adenosyl-L-homocysteine · ligand · chains E, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.86 | 0.87 | 53 | empty |
| 2 | 1149 | 0.82 | 0.83 | 111 | empty |
| 3 | 384 | 0.76 | 0.86 | 49 | NAD |
| 4 | 255 | 0.76 | 0.89 | 39 | SAH |
| 5 | 408 | 0.73 | 0.83 | 50 | NAD |
Interfaces
12 interfaces between chains.
- A–B · 1972 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1928 Ų buried · 14 hydrogen bonds · protein-protein
- E–T · 1841 Ų buried · 40 hydrogen bonds · protein-nucleic
- B–C · 1548 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1531 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- Q99714 · AlphaFold monomer V2.0 prediction for 3-hydroxyacyl-CoA dehydrogenase type-2 (Q99714) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q7L0Y3 · AlphaFold monomer V2.0 prediction for tRNA methyltransferase 10 homolog C (Q7L0Y3) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q99714
- Every structure of UniProt Q7L0Y3
- Elsewhere: RCSB PDB 8CBO · PDBe 8CBO · UniProt Q99714 · UniProt Q7L0Y3
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