MolNFT v2 · #188004 · protein
ThyX reconstituted with N5-carbinolamine flavin
7NDZ · Flavin-dependent thymidylate synthase: “ThyX reconstituted with N5-carbinolamine flavin”. X-ray diffraction at 2.7, 2 ligands (HUF, FDA), 6 pockets (best druggability 0.86). MolNFT v2 #188004 on GenesisL1: 3D structure, binding…
- PDB
- 7NDZ
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Thermotoga maritima
- Molecule
- Flavin-dependent thymidylate synthase
- EC
- 2.1.1.148
- UniProt
- Q9WYT0
- Ligands
- HUF, FDA
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.7 · 4 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 216 | 51% helix, 18% strand | Q9WYT0 |
| B | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 216 | 51% helix, 18% strand | Q9WYT0 |
| C | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 217 | 51% helix, 18% strand | Q9WYT0 |
| D | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 210 | 51% helix, 18% strand | Q9WYT0 |
Ligands and binding sites
- HUF · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate · ligand · 3 copies · chains A, C, D, B
- FDA · Dihydroflavine-adenine dinucleotide · ligand · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.86 | 0.91 | 64 | FDA, HUF |
| 2 | 225 | 0.75 | 0.90 | 38 | HUF, PEG |
| 3 | 191 | 0.75 | 0.91 | 34 | HUF |
| 4 | 182 | 0.71 | 0.89 | 29 | FDA, PEG |
| 5 | 119 | 0.70 | 0.91 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2215 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2089 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1253 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1195 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7NDZ · Thyx reconstituted with N5-carbinolamine flavin · 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 Q9WYT0
- Elsewhere: RCSB PDB 7NDZ · PDBe 7NDZ · UniProt Q9WYT0
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