Research workbench
Cryo-EM structure of the ribosome-nata complex
Analyse Cryo-EM structure of the ribosome-nata complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HD5
- Type
- protein
- Length
- 1,234 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal acetyltransferase a complex subunit NAT1; N-terminal acetyltransferase a…
- EC
- 2.3.1.255, 2.3.1.258
- UniProt
- P12945, P07347, Q08689
- Pockets
- 15 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| t | N-terminal acetyltransferase a complex subunit NAT1 | protein | 838 | 69% helix, 0% strand | P12945 |
| u | N-terminal acetyltransferase a complex catalytic subunit ARD1 (EC 2.3.1.255) | protein | 235 | 21% helix, 20% strand | P07347 |
| v | N-alpha-acetyltransferase NAT5 (EC 2.3.1.258) | protein | 161 | 22% helix, 33% strand | Q08689 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.84 | 0.85 | 91 | empty |
| 2 | 1070 | 0.82 | 0.83 | 109 | empty |
| 3 | 657 | 0.80 | 0.85 | 60 | empty |
| 4 | 57 | 0.68 | 0.96 | 16 | empty |
| 5 | 366 | 0.66 | 0.79 | 41 | empty |
Interfaces
3 interfaces between chains.
- t–u · 4365 Ų buried · 52 hydrogen bonds · protein-protein
- t–v · 752 Ų buried · 10 hydrogen bonds · protein-protein
- u–v · 245 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6HD5 · Cryo-EM structure of the ribosome-NatA complex · the same entry in another collection · chain t against t, TM-score 1.00
- P12945 · AlphaFold monomer V2.0 prediction for N-terminal acetyltransferase a complex subunit NAT1… · a predicted model of the same protein · chain t against A, TM-score 0.96
- Q08689 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase NAT5 (Q08689) · a predicted model of the same protein · chain v against A, TM-score 0.94
- P07347 · AlphaFold monomer V2.0 prediction for N-terminal acetyltransferase a complex catalytic… · a predicted model of the same protein · chain u against A, TM-score 0.77
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 P12945
- Every structure of UniProt P07347
- Every structure of UniProt Q08689
- Elsewhere: RCSB PDB 6HD5 · PDBe 6HD5 · UniProt P12945 · UniProt P07347 · UniProt Q08689
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