Research workbench
Crystal structure of the natc complex bound to CoA
Analyse Crystal structure of the natc complex bound to CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YGB
- Type
- protein
- Length
- 961 residues
- Chains
- 3
- Method
- x-ray diffraction
- 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
- Q03503, Q02197, P23059
- Ligands
- COA, IOD, CL
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 30 (EC 2.3.1.256) | protein | 159 | 35% helix, 34% strand | Q03503 |
| B | N-alpha-acetyltransferase 35, natc auxiliary subunit | protein | 725 | 64% helix, 4% strand | Q02197 |
| C | N-alpha-acetyltransferase 38, natc auxiliary subunit | protein | 77 | 14% helix, 56% strand | P23059 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains A
- IOD · Iodide ion · ion · 9 copies · chains A, B, C
- CL · Chloride ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.83 | 0.97 | 32 | PEG, EDO |
| 2 | 972 | 0.74 | 0.77 | 94 | COA, EDO, IOD, CL |
| 3 | 300 | 0.57 | 0.77 | 29 | IOD |
| 4 | 254 | 0.57 | 0.77 | 38 | PEG, IOD |
| 5 | 92 | 0.55 | 0.85 | 21 | EDO |
Interfaces
3 interfaces between chains.
- B–C · 2084 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2004 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6YGB · Crystal structure of the NatC complex bound to CoA · the same entry in another collection · chain A against A, TM-score 1.00
- P23059 · 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 0.98
- Q02197 · 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 0.96
- Q03503 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 30 (Q03503) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q03503
- Every structure of UniProt Q02197
- Every structure of UniProt P23059
- Elsewhere: RCSB PDB 6YGB · PDBe 6YGB · UniProt Q03503 · UniProt Q02197 · UniProt P23059
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