Research workbench
The natb acetyltransferase complex bound to bisubstrate inhibitor
Analyse The natb acetyltransferase complex bound to bisubstrate inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K18
- Type
- protein
- Length
- 1,777 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; N-terminal acetyltransferase B complex subunit NAT3; Bisubstrate…
- UniProt
- C4YFL7, C4YDZ9
- Ligands
- COA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 715 | 71% helix, 1% strand | C4YFL7 |
| B | N-terminal acetyltransferase B complex subunit NAT3 | protein | 179 | 30% helix, 28% strand | C4YDZ9 |
| C | Uncharacterized protein | protein | 696 | 71% helix, 1% strand | C4YFL7 |
| D | N-terminal acetyltransferase B complex subunit NAT3 | protein | 177 | 32% helix, 28% strand | C4YDZ9 |
| F | Bisubstrate inhibitor | protein | 6 | 0% helix, 0% strand | — |
| E | Bisubstrate inhibitor | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains C, D, F, A, B, E
- ACY · Acetic acid · additive · 2 copies · chains D, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.81 | 0.88 | 65 | empty |
| 2 | 761 | 0.78 | 0.82 | 93 | COA, ACY |
| 3 | 744 | 0.77 | 0.82 | 79 | COA, ACY |
| 4 | 412 | 0.75 | 0.85 | 56 | empty |
| 5 | 226 | 0.68 | 0.85 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2512 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2496 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 501 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 407 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
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 C4YFL7
- Every structure of UniProt C4YDZ9
- Elsewhere: RCSB PDB 5K18 · PDBe 5K18 · UniProt C4YFL7 · UniProt C4YDZ9
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