MolNFT v1 · #114906 · protein
Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg and thymine (T)
5C3Q · Thymine dioxygenase: “Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg and thymine (T)”. X-ray diffraction, 3 ligands (AKG, TDR, NI), 12 pockets (best druggability 0.82). MolNFT v1 #114906 on…
- PDB
- 5C3Q
- Type
- protein
- Length
- 1,288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymine dioxygenase
- UniProt
- Q7RYZ9
- Ligands
- AKG, TDR, NI
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymine dioxygenase | protein | 335 | 32% helix, 21% strand | Q7RYZ9 |
| B, C | Thymine dioxygenase | protein | 311 | 32% helix, 23% strand | Q7RYZ9 |
| D | Thymine dioxygenase | protein | 331 | 32% helix, 22% strand | Q7RYZ9 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- TDR · Thymine · 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 · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.82 | 0.88 | 56 | EDO |
| 2 | 747 | 0.81 | 0.85 | 89 | EDO |
| 3 | 1193 | 0.76 | 0.79 | 119 | NI, AKG, TDR, EDO |
| 4 | 433 | 0.73 | 0.83 | 58 | AKG, TDR |
| 5 | 296 | 0.71 | 0.85 | 55 | NI, AKG, TDR |
Interfaces
4 interfaces between chains.
- A–B · 1116 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 489 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 172 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5C3Q · 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 5C3Q · PDBe 5C3Q · UniProt Q7RYZ9
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