MolNFT v1 · #28316 · protein
Complex of bacillus subtilis tena with 4-amino-2-methyl-5- hydroxymethylpyrimidine
1YAK · Transcriptional activator tena: “Complex of bacillus subtilis tena with 4-amino-2-methyl-5- hydroxymethylpyrimidine”. X-ray diffraction, 1 ligand (HMH), 20 pockets (best druggability 0.79). MolNFT v1 #28316 on GenesisL1: 3D…
- PDB
- 1YAK
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator tena
- UniProt
- P25052
- Ligands
- HMH
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transcriptional activator tena | protein | 219 | 81% helix, 0% strand | P25052 |
| B | Transcriptional activator tena | protein | 218 | 77% helix, 0% strand | P25052 |
| C | Transcriptional activator tena | protein | 220 | 73% helix, 0% strand | P25052 |
Ligands and binding sites
- HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.79 | 0.92 | 35 | HMH |
| 2 | 233 | 0.79 | 0.92 | 34 | HMH |
| 3 | 111 | 0.74 | 0.94 | 22 | HMH |
| 4 | 131 | 0.72 | 0.91 | 24 | HMH |
| 5 | 60 | 0.68 | 0.95 | 14 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1112 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1013 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 56 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1YAK · Complex of Bacillus subtilis TenA with 4-amino-2-methyl-5-hydroxymethylpyrimidine · the same entry in another collection · chain A against A, TM-score 1.00
- P25052 · AlphaFold monomer V2.0 prediction for aminopyrimidine aminohydrolase (P25052) · a predicted model of the same protein · 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 P25052
- Elsewhere: RCSB PDB 1YAK · PDBe 1YAK · UniProt P25052
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