MolNFT v1 · #28280 · protein
Crystal structure of bacillus subtilis protein yhfp with NAD bound
1Y9E · Hypothetical protein yhfp: “Crystal structure of bacillus subtilis protein yhfp with NAD bound”. X-ray diffraction, 1 ligand (NAD), 8 pockets (best druggability 0.83). MolNFT v1 #28280 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1Y9E
- Type
- protein
- Length
- 1,974 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yhfp
- UniProt
- O07615
- Ligands
- NAD
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hypothetical protein yhfp | protein | 329 | 29% helix, 25% strand | O07615 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.83 | 0.84 | 134 | empty |
| 2 | 1059 | 0.83 | 0.84 | 109 | NAD |
| 3 | 1177 | 0.83 | 0.84 | 130 | empty |
| 4 | 1183 | 0.82 | 0.83 | 116 | NAD |
| 5 | 1169 | 0.81 | 0.83 | 110 | NAD |
Interfaces
12 interfaces between chains.
- C–F · 1184 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 1160 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1149 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 473 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 447 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1Y9E · Crystal structure of Bacillus subtilis protein yhfP with NAD bound · the same entry in another collection · chain C against C, TM-score 1.00
- O07615 · AlphaFold monomer V2.0 prediction for putative quinone oxidoreductase yhfp (O07615) · 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 O07615
- Elsewhere: RCSB PDB 1Y9E · PDBe 1Y9E · UniProt O07615
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