MolNFT v1 · #181473 · protein
Crystal structure of ado
7LVZ · 2-aminoethanethiol dioxygenase: “Crystal structure of ado”. X-ray diffraction, 3 ligands (FE2, MG, CL), 13 pockets (best druggability 0.76). MolNFT v1 #181473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LVZ
- Type
- protein
- Length
- 965 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-aminoethanethiol dioxygenase
- EC
- 1.13.11.19
- UniProt
- Q6PDY2
- Ligands
- FE2, MG, CL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-aminoethanethiol dioxygenase (EC 1.13.11.19) | protein | 236 | 16% helix, 39% strand | Q6PDY2 |
| B | 2-aminoethanethiol dioxygenase (EC 1.13.11.19) | protein | 245 | 17% helix, 39% strand | Q6PDY2 |
| C | 2-aminoethanethiol dioxygenase (EC 1.13.11.19) | protein | 238 | 16% helix, 39% strand | Q6PDY2 |
| D | 2-aminoethanethiol dioxygenase (EC 1.13.11.19) | protein | 246 | 16% helix, 37% strand | Q6PDY2 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.76 | 0.82 | 68 | empty |
| 2 | 716 | 0.73 | 0.79 | 76 | empty |
| 3 | 318 | 0.67 | 0.82 | 46 | empty |
| 4 | 165 | 0.55 | 0.80 | 24 | FE2 |
| 5 | 165 | 0.53 | 0.79 | 24 | FE2 |
Interfaces
5 interfaces between chains.
- A–D · 1017 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 916 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 560 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 130 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q6PDY2
- Elsewhere: RCSB PDB 7LVZ · PDBe 7LVZ · UniProt Q6PDY2
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