MolNFT v1 · #57315 · protein
Crystal structure of mqnd (TTHA1568), a menaquinone biosynthetic enzyme from thermus thermophilus HB8
3A3U: “Crystal structure of mqnd (TTHA1568), a menaquinone biosynthetic enzyme from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (K), 3 pockets (best druggability 0.77). MolNFT v1 #57315 on GenesisL1: 3D structure, binding sites…
- PDB
- 3A3U
- Type
- protein
- Length
- 270 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menaquinone biosynthetic enzyme
- UniProt
- Q5SI12
- Ligands
- K
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Menaquinone biosynthetic enzyme | protein | 270 | 46% helix, 19% strand | Q5SI12 |
Ligands and binding sites
- K · Potassium ion · metal · chains A
- TLA · L(+)-tartaric acid · additive · chains A
- 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.77 | 0.98 | 24 | TLA |
| 2 | 93 | 0.38 | 0.76 | 27 | empty |
| 3 | 57 | 0.37 | 0.79 | 13 | empty |
Compared structures
- 3A3U · Crystal structure of MqnD (TTHA1568), a menaqui biosynthetic enzyme from Thermus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SI12 · AlphaFold monomer V2.0 prediction for 1,4-dihydroxy-6-naphtoate synthase (Q5SI12) · 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 Q5SI12
- Elsewhere: RCSB PDB 3A3U · PDBe 3A3U · UniProt Q5SI12
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