MolNFT v1 · #140534 · protein
Crystal structure of tetr family repressor alkx from dietzia sp. strain DQ12-45-1B implicated in biodegradation of N-alkanes
5YDP · Tetr transcriptional regulatory protein: “Crystal structure of tetr family repressor alkx from dietzia sp. strain DQ12-45-1B implicated in…”. X-ray diffraction, 11 pockets (best druggability 0.83). MolNFT v1 #140534 on GenesisL1: 3D…
- PDB
- 5YDP
- Type
- protein
- Length
- 543 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetr transcriptional regulatory protein
- UniProt
- G3EIL4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetr transcriptional regulatory protein | protein | 184 | 77% helix, 0% strand | G3EIL4 |
| B | Tetr transcriptional regulatory protein | protein | 181 | 76% helix, 0% strand | G3EIL4 |
| C | Tetr transcriptional regulatory protein | protein | 178 | 75% helix, 0% strand | G3EIL4 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.83 | 0.98 | 32 | empty |
| 2 | 165 | 0.82 | 0.96 | 33 | empty |
| 3 | 231 | 0.75 | 0.89 | 34 | empty |
| 4 | 61 | 0.69 | 0.97 | 20 | empty |
| 5 | 178 | 0.46 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1467 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 330 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5YDP · Crystal Structure of TetR Family Repressor AlkX from Dietzia sp. Strain DQ12-45-1b… · 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 G3EIL4
- Elsewhere: RCSB PDB 5YDP · PDBe 5YDP · UniProt G3EIL4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.