MolNFT v1 · #81403 · protein
Crystal structure of the brucella abortus enzyme catalyzing the first committed step of the methylerythritol 4-phosphate pathway.
3UPL · Oxidoreductase: “Crystal structure of the brucella abortus enzyme catalyzing the first committed step of the methylerythritol…”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.82). MolNFT v1 #81403 on GenesisL1: 3D…
- PDB
- 3UPL
- Type
- protein
- Length
- 874 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase
- UniProt
- Q2YIM3
- Ligands
- MG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 437 | 41% helix, 20% strand | Q2YIM3 |
| B | Oxidoreductase | protein | 437 | 41% helix, 20% strand | Q2YIM3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.82 | 0.85 | 74 | GOL |
| 2 | 943 | 0.79 | 0.81 | 88 | MG |
| 3 | 920 | 0.78 | 0.81 | 81 | empty |
| 4 | 357 | 0.60 | 0.77 | 38 | empty |
| 5 | 52 | 0.35 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2862 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3UPL · Crystal structure of the Brucella abortus enzyme catalyzing the first committed step of… · 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 Q2YIM3
- Elsewhere: RCSB PDB 3UPL · PDBe 3UPL · UniProt Q2YIM3
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