MolNFT v1 · #61724 · protein
Crystal structure of an oxidoreductase from pseudomonas syringae
3DTY · Oxidoreductase, GFO/IDH/MOCA family: “Crystal structure of an oxidoreductase from pseudomonas syringae”. X-ray diffraction, 1 ligand (MG), 19 pockets (best druggability 0.81). MolNFT v1 #61724 on GenesisL1: 3D structure, binding…
- PDB
- 3DTY
- Type
- protein
- Length
- 1,474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, GFO/IDH/MOCA family
- UniProt
- Q880Y1
- Ligands
- MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Oxidoreductase, GFO/IDH/MOCA family | protein | 374 | 37% helix, 23% strand | Q880Y1 |
| B | Oxidoreductase, GFO/IDH/MOCA family | protein | 364 | 39% helix, 23% strand | Q880Y1 |
| D | Oxidoreductase, GFO/IDH/MOCA family | protein | 362 | 38% helix, 24% strand | Q880Y1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.81 | 0.86 | 75 | empty |
| 2 | 659 | 0.81 | 0.86 | 74 | empty |
| 3 | 867 | 0.72 | 0.77 | 74 | empty |
| 4 | 50 | 0.70 | 0.98 | 16 | empty |
| 5 | 709 | 0.70 | 0.77 | 66 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1487 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1381 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1240 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 404 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 3DTY · Crystal structure of an Oxidoreductase from Pseudomonas syringae · 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 Q880Y1
- Elsewhere: RCSB PDB 3DTY · PDBe 3DTY · UniProt Q880Y1
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