MolNFT v1 · #114908 · protein
Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg and 5-formyluracil (5FU)
5C3S · Thymine dioxygenase: “Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg and 5-formyluracil (5FU)”. X-ray diffraction, 3 ligands (AKG, FYU, NI), 15 pockets (best druggability 0.81). MolNFT v1 #114908…
- PDB
- 5C3S
- Type
- protein
- Length
- 1,284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymine dioxygenase
- UniProt
- Q7RYZ9
- Ligands
- AKG, FYU, NI
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymine dioxygenase | protein | 334 | 32% helix, 21% strand | Q7RYZ9 |
| B | Thymine dioxygenase | protein | 310 | 32% helix, 23% strand | Q7RYZ9 |
| C | Thymine dioxygenase | protein | 311 | 32% helix, 23% strand | Q7RYZ9 |
| D | Thymine dioxygenase | protein | 329 | 33% helix, 22% strand | Q7RYZ9 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- FYU · 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.81 | 0.83 | 92 | empty |
| 2 | 615 | 0.81 | 0.86 | 62 | EDO |
| 3 | 504 | 0.74 | 0.82 | 66 | NI, AKG, FYU |
| 4 | 325 | 0.72 | 0.84 | 53 | NI, AKG, FYU |
| 5 | 351 | 0.69 | 0.82 | 44 | NI, AKG, FYU |
Interfaces
5 interfaces between chains.
- A–B · 1149 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 393 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 250 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5C3S · Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG and… · 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 Q7RYZ9
- Elsewhere: RCSB PDB 5C3S · PDBe 5C3S · UniProt Q7RYZ9
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