MolNFT v1 · #100515 · protein
Crystal structure of fdtd, a bifunctional KETOISOMERASE/N- acetyltransferase from shewanella denitrificans
4MZU · Wxcm-like protein: “Crystal structure of fdtd, a bifunctional KETOISOMERASE/N- acetyltransferase from shewanella denitrificans”. X-ray diffraction, 4 ligands (COA, TYD, TDR), 20 pockets (best druggability 0.73). MolNFT v1 #100515 on…
- PDB
- 4MZU
- Type
- protein
- Length
- 3,415 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wxcm-like protein
- UniProt
- Q12KT8
- Ligands
- COA, TYD, TDR, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 12 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wxcm-like protein | protein | 285 | 4% helix, 42% strand | Q12KT8 |
| B | Wxcm-like protein | protein | 290 | 4% helix, 42% strand | Q12KT8 |
| C | Wxcm-like protein | protein | 285 | 5% helix, 42% strand | Q12KT8 |
| D | Wxcm-like protein | protein | 283 | 5% helix, 43% strand | Q12KT8 |
| E | Wxcm-like protein | protein | 286 | 2% helix, 41% strand | Q12KT8 |
| F | Wxcm-like protein | protein | 294 | 6% helix, 41% strand | Q12KT8 |
| G | Wxcm-like protein | protein | 283 | 4% helix, 43% strand | Q12KT8 |
| H | Wxcm-like protein | protein | 278 | 3% helix, 44% strand | Q12KT8 |
| I | Wxcm-like protein | protein | 285 | 5% helix, 42% strand | Q12KT8 |
| J | Wxcm-like protein | protein | 275 | 3% helix, 44% strand | Q12KT8 |
| K | Wxcm-like protein | protein | 285 | 5% helix, 43% strand | Q12KT8 |
| L | Wxcm-like protein | protein | 286 | 6% helix, 42% strand | Q12KT8 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 12 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- TYD · Thymidine-5'-diphosphate · ligand · 12 copies · chains A, E, B, D, C, F, G, K, H, J, I, L
- TDR · Thymine · ligand · 9 copies · chains A, B, C, D, E, F, J, K, L
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E, F, G, H, I, J, K, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.99 | 29 | MG |
| 2 | 59 | 0.72 | 0.99 | 24 | MG |
| 3 | 56 | 0.72 | 0.99 | 25 | MG |
| 4 | 308 | 0.61 | 0.78 | 47 | TDR, COA |
| 5 | 215 | 0.60 | 0.81 | 45 | TYD |
Interfaces
19 interfaces between chains.
- G–K · 1697 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 1681 Ų buried · 31 hydrogen bonds · protein-protein
- H–J · 1675 Ų buried · 34 hydrogen bonds · protein-protein
- I–L · 1669 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1668 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4MZU · Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from… · 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 Q12KT8
- Elsewhere: RCSB PDB 4MZU · PDBe 4MZU · UniProt Q12KT8
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