Research workbench
Crystal structure of the full-length neurospora crassa T7H in complex with alpha-kg and 5-hydroxymethyluracil (5HMU)
Analyse Crystal structure of the full-length neurospora crassa T7H in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C3R
- 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, HMU, NI
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymine dioxygenase | protein | 333 | 33% helix, 22% strand | Q7RYZ9 |
| B, C | Thymine dioxygenase | protein | 310 | 32% helix, 23% strand | Q7RYZ9 |
| D | Thymine dioxygenase | protein | 329 | 33% helix, 23% strand | Q7RYZ9 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- HMU · 5-hydroxymethyl uracil · 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 · 13 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.81 | 0.86 | 61 | EDO |
| 2 | 906 | 0.80 | 0.83 | 79 | EDO |
| 3 | 527 | 0.74 | 0.82 | 64 | NI, AKG, HMU |
| 4 | 637 | 0.73 | 0.80 | 59 | empty |
| 5 | 357 | 0.73 | 0.85 | 55 | AKG, HMU |
Interfaces
5 interfaces between chains.
- A–B · 1129 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 359 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 241 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 155 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5C3R · 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 5C3R · PDBe 5C3R · UniProt Q7RYZ9
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