Research workbench
Cryo-EM structure of S. pombe natc complex with a bisubstrate inhibitor and inositol hexaphosphate
Analyse Cryo-EM structure of S. pombe natc complex with a bisubstrate inhibitor and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L1K
- Type
- protein
- Length
- 883 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 30; N-alpha-acetyltransferase 35, natc auxiliary subunit…
- EC
- 2.3.1.256
- UniProt
- O74311, Q9USY3, O43080
- Ligands
- IHP, CMC
- Pockets
- 10 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 30 (EC 2.3.1.256) | protein | 149 | 23% helix, 29% strand | O74311 |
| B | N-alpha-acetyltransferase 35, natc auxiliary subunit | protein | 660 | 51% helix, 2% strand | Q9USY3 |
| C | N-alpha-acetyltransferase 38, natc auxiliary subunit | protein | 70 | 14% helix, 40% strand | O43080 |
| D | Mlgp peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, B
- CMC · Carboxymethyl coenzyme *A · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.84 | 0.97 | 23 | empty |
| 2 | 573 | 0.68 | 0.78 | 71 | empty |
| 3 | 510 | 0.64 | 0.76 | 64 | IHP |
| 4 | 194 | 0.57 | 0.80 | 28 | CMC |
| 5 | 125 | 0.51 | 0.80 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1999 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1822 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 399 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 229 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7L1K · Cryo-EM structure of S. Pombe NatC complex with a Bisubstrate inhibitor and inositol… · the same entry in another collection · chain A against A, TM-score 1.00
- O74311 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 30 (O74311) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9USY3 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 35, natc auxiliary… · a predicted model of the same protein · chain B against A, TM-score 0.97
- O43080 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 38, natc auxiliary… · a predicted model of the same protein · chain C against A, TM-score 0.92
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 O74311
- Every structure of UniProt Q9USY3
- Every structure of UniProt O43080
- Elsewhere: RCSB PDB 7L1K · PDBe 7L1K · UniProt O74311 · UniProt Q9USY3 · UniProt O43080
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