MolNFT v1 · #128350 · protein
Structure of NAA15/NAA10 bound to hypk-thb
5NNP · N-terminal acetyltransferase-like protein: “Structure of NAA15/NAA10 bound to hypk-thb”. X-ray diffraction, 2 ligands (CMC, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #128350 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NNP
- Type
- protein
- Length
- 1,778 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal acetyltransferase-like protein; Putative uncharacterized protein…
- UniProt
- G0S4M4, G0SEE8, G0SCY6
- Ligands
- CMC, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-terminal acetyltransferase-like protein | protein | 665 | 75% helix, 0% strand | G0S4M4 |
| B | Putative uncharacterized protein | protein | 179 | 40% helix, 27% strand | G0SEE8 |
| C, G | Putative uncharacterized protein | protein | 45 | 62% helix, 0% strand | G0SCY6 |
| E | N-terminal acetyltransferase-like protein | protein | 658 | 76% helix, 0% strand | G0S4M4 |
| F | Putative uncharacterized protein | protein | 178 | 41% helix, 25% strand | G0SEE8 |
| I, L | Ser-glu-ser-ser | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- CMC · Carboxymethyl coenzyme *A · ligand · 2 copies · chains A, B, I, E, F, L
- PO4 · Phosphate ion · ion · 4 copies · chains A, E, F
- GOL · Glycerol · additive · 27 copies · chains A, B, C, E, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.79 | 0.81 | 95 | CMC |
| 2 | 818 | 0.76 | 0.80 | 56 | GOL, PO4 |
| 3 | 843 | 0.76 | 0.80 | 57 | GOL, PO4 |
| 4 | 583 | 0.73 | 0.81 | 51 | GOL, CMC |
| 5 | 562 | 0.65 | 0.76 | 46 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3080 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2999 Ų buried · 38 hydrogen bonds · protein-protein
- E–G · 838 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 9 hydrogen bonds · protein-protein
- F–L · 374 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, formylation).
Compared structures
- 5NNP · Structure of Naa15/Naa10 bound to HypK-THB · the same entry in another collection · chain A against A, TM-score 1.00
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 G0S4M4
- Every structure of UniProt G0SEE8
- Every structure of UniProt G0SCY6
- Elsewhere: RCSB PDB 5NNP · PDBe 5NNP · UniProt G0S4M4 · UniProt G0SEE8 · UniProt G0SCY6
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