Research workbench
Thyx-FADH2 soaked with 20 mm formaldehyde
Analyse Thyx-FADH2 soaked with 20 mm formaldehyde in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NDW
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin-dependent thymidylate synthase
- EC
- 2.1.1.148
- UniProt
- Q9WYT0
- Ligands
- HUF, FDA, PO4
- Pockets
- 3 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 211 | 52% helix, 18% strand | Q9WYT0 |
| B | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 211 | 52% helix, 18% strand | Q9WYT0 |
| C | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 216 | 52% helix, 18% strand | Q9WYT0 |
| D | Flavin-dependent thymidylate synthase (EC 2.1.1.148) | protein | 218 | 50% 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 · 2 copies · chains A, C, D, B
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, A, D
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.89 | 0.90 | 123 | HUF, FDA, PG4, PO4, PEG |
| 2 | 334 | 0.80 | 0.91 | 43 | HUF, PO4, PEG |
| 3 | 119 | 0.67 | 0.90 | 21 | PO4 |
Interfaces
6 interfaces between chains.
- B–C · 2166 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2127 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1381 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1157 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 246 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7NDW · ThyX-FADH2 soaked with 20 mM Formaldehyde · 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 7NDW · PDBe 7NDW · UniProt Q9WYT0
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