MolNFT v1 · #69101 · protein + RNA
Crystal structure of the transamidosome
3KFU · Non-discriminating and archaeal-type aspartyl-tRNA…: “Crystal structure of the transamidosome”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.77). MolNFT v1 #69101 on GenesisL1: 3D structure, binding sites…
- PDB
- 3KFU
- Type
- protein + RNA
- Length
- 3,784 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-discriminating and archaeal-type aspartyl-tRNA synthetase; Glutamyl-TRNA(GLN)…
- EC
- 6.3.5.-
- UniProt
- Q5SIC2, Q9LCX3, Q9LCX2, Q9LCX4
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 12 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-discriminating and archaeal-type aspartyl-tRNA synthetase | protein | 374 | 38% helix, 28% strand | Q5SIC2 |
| B | Non-discriminating and archaeal-type aspartyl-tRNA synthetase | protein | 376 | 37% helix, 28% strand | Q5SIC2 |
| C | Non-discriminating and archaeal-type aspartyl-tRNA synthetase | protein | 377 | 37% helix, 28% strand | Q5SIC2 |
| D | Non-discriminating and archaeal-type aspartyl-tRNA synthetase | protein | 372 | 37% helix, 28% strand | Q5SIC2 |
| E | Glutamyl-TRNA(GLN) amidotransferase subunit a (EC 6.3.5.-) | protein | 468 | 38% helix, 15% strand | Q9LCX3 |
| F | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit B (EC 6.3.5.-) | protein | 447 | 38% helix, 19% strand | Q9LCX2 |
| G | Glutamyl-TRNA(GLN) amidotransferase subunit C (EC 6.3.5.-) | protein | 86 | 40% helix, 8% strand | Q9LCX4 |
| H | Glutamyl-TRNA(GLN) amidotransferase subunit a (EC 6.3.5.-) | protein | 467 | 38% helix, 14% strand | Q9LCX3 |
| I | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit B (EC 6.3.5.-) | protein | 444 | 38% helix, 20% strand | Q9LCX2 |
| J | Glutamyl-TRNA(GLN) amidotransferase subunit C (EC 6.3.5.-) | protein | 83 | 41% helix, 8% strand | Q9LCX4 |
| K, L | TRNA-asn | rna | 74 | — | — |
| M, N | TRNA-asn | rna | 71 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.77 | 0.80 | 66 | empty |
| 2 | 1041 | 0.77 | 0.79 | 82 | empty |
| 3 | 981 | 0.77 | 0.79 | 92 | empty |
| 4 | 573 | 0.73 | 0.81 | 32 | empty |
| 5 | 589 | 0.72 | 0.81 | 35 | empty |
Interfaces
30 interfaces between chains.
- A–B · 3125 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 3119 Ų buried · 44 hydrogen bonds · protein-protein
- E–G · 2351 Ų buried · 19 hydrogen bonds · protein-protein
- H–J · 2343 Ų buried · 16 hydrogen bonds · protein-protein
- F–L · 1912 Ų buried · 41 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (nucleotide modification).
Compared structures
- 3KFU · Crystal structure of the transamidosome · the same entry in another collection · chain N against N, 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 Q5SIC2
- Every structure of UniProt Q9LCX3
- Every structure of UniProt Q9LCX2
- Every structure of UniProt Q9LCX4
- Elsewhere: RCSB PDB 3KFU · PDBe 3KFU · UniProt Q5SIC2 · UniProt Q9LCX3 · UniProt Q9LCX2 · UniProt Q9LCX4
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