MolNFT v1 · #170700 · protein
Crystal structure of the natc complex bound to gag peptide and CoA
6YGD · N-alpha-acetyltransferase 30: “Crystal structure of the natc complex bound to gag peptide and CoA”. X-ray diffraction, 3 ligands (COA, IOD, CL), 14 pockets (best druggability 0.84). MolNFT v1 #170700 on GenesisL1: 3D structure…
- PDB
- 6YGD
- Type
- protein
- Length
- 956 residues
- Chains
- 4
- 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, P32503
- Ligands
- COA, IOD, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 30 (EC 2.3.1.256) | protein | 159 | 33% helix, 34% strand | Q03503 |
| B | N-alpha-acetyltransferase 35, natc auxiliary subunit | protein | 720 | 62% helix, 4% strand | Q02197 |
| C | N-alpha-acetyltransferase 38, natc auxiliary subunit | protein | 71 | 17% helix, 61% strand | P23059 |
| D | Major capsid protein | protein | 6 | 0% helix, 0% strand | P32503 |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains A, D
- IOD · Iodide ion · ion · 10 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.84 | 0.97 | 32 | CL, EDO |
| 2 | 514 | 0.73 | 0.81 | 66 | IOD |
| 3 | 57 | 0.63 | 0.93 | 16 | IOD |
| 4 | 59 | 0.60 | 0.91 | 19 | CL |
| 5 | 101 | 0.56 | 0.84 | 21 | CL |
Interfaces
5 interfaces between chains.
- B–C · 2055 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1907 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 211 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YGD · Crystal structure of the NatC complex bound to Gag peptide and CoA · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.98
- 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
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
- Every structure of UniProt P32503
- Elsewhere: RCSB PDB 6YGD · PDBe 6YGD · UniProt Q03503 · UniProt Q02197 · UniProt P23059 · UniProt P32503
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