MolNFT v1 · #114905 · protein
Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg
5C3P · Thymine dioxygenase: “Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg”. X-ray diffraction, 2 ligands (AKG, NI), 15 pockets (best druggability 0.85). MolNFT v1 #114905 on GenesisL1: 3D structure…
- PDB
- 5C3P
- Type
- protein
- Length
- 1,282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymine dioxygenase
- UniProt
- Q7RYZ9
- Ligands
- AKG, NI
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymine dioxygenase | protein | 329 | 31% helix, 22% strand | Q7RYZ9 |
| B | Thymine dioxygenase | protein | 325 | 31% helix, 22% strand | Q7RYZ9 |
| C | Thymine dioxygenase | protein | 325 | 34% helix, 22% strand | Q7RYZ9 |
| D | Thymine dioxygenase | protein | 303 | 32% helix, 24% strand | Q7RYZ9 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · 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 · 15 copies · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.85 | 0.86 | 117 | NI, AKG, EDO |
| 2 | 1038 | 0.83 | 0.84 | 115 | EDO |
| 3 | 348 | 0.73 | 0.85 | 52 | AKG |
| 4 | 355 | 0.73 | 0.85 | 53 | AKG |
| 5 | 295 | 0.71 | 0.85 | 47 | NI, AKG |
Interfaces
5 interfaces between chains.
- A–C · 1052 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 518 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 356 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 184 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C3P · Crystal structure of the full-length Neurospora crassa T7H in complex with alpha-KG · 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 5C3P · PDBe 5C3P · UniProt Q7RYZ9
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