Research workbench
Crystal structure of human natf (HNAA60) bound to a bisubstrate analogue
Analyse Crystal structure of human natf (HNAA60) bound to a bisubstrate analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICV
- Type
- protein
- Length
- 368 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 60; Met-lys-ala-val-lig
- EC
- 2.3.1.48, 2.3.1.88
- UniProt
- Q9H7X0
- Ligands
- 1XE
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-alpha-acetyltransferase 60 (EC 2.3.1.48, 2.3.1.88) | protein | 180 | 33% helix, 37% strand | Q9H7X0 |
| C, D | Met-lys-ala-val-lig | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1XE · [5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.72 | 0.77 | 65 | empty |
| 2 | 215 | 0.59 | 0.80 | 26 | 1XE |
| 3 | 211 | 0.59 | 0.80 | 25 | 1XE |
Interfaces
3 interfaces between chains.
- A–C · 414 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 411 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5ICV · Crystal structure of human NatF (hNaa60) bound to a bisubstrate analogue · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H7X0 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 60 (Q9H7X0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9H7X0
- Elsewhere: RCSB PDB 5ICV · PDBe 5ICV · UniProt Q9H7X0
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