MolNFT v1 · #77851 · protein
Crystal structure of enolase PRK14017 (target efi-500653) from ralstonia pickettii 12J with magnesium bound
3RRA · Putative D-galactonate dehydratase: “Crystal structure of enolase PRK14017 (target efi-500653) from ralstonia pickettii 12J with magnesium bound”. X-ray diffraction, 2 ligands (MG, CL), 8 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 3RRA
- Type
- protein
- Length
- 753 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative D-galactonate dehydratase
- EC
- 4.2.1.6
- UniProt
- B2UCA8
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative D-galactonate dehydratase (EC 4.2.1.6) | protein | 374 | 40% helix, 17% strand | B2UCA8 |
| B | Putative D-galactonate dehydratase (EC 4.2.1.6) | protein | 379 | 39% helix, 17% strand | B2UCA8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.85 | 0.88 | 60 | empty |
| 2 | 425 | 0.67 | 0.79 | 51 | empty |
| 3 | 227 | 0.57 | 0.79 | 34 | empty |
| 4 | 128 | 0.42 | 0.75 | 24 | empty |
| 5 | 65 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2279 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3RRA · Crystal structure of enolase PRK14017 (target EFI-500653) from Ralstonia pickettii 12J… · the same entry in another collection · chain A against A, TM-score 1.00
- B2UCA8 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase (B2UCA8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 B2UCA8
- Elsewhere: RCSB PDB 3RRA · PDBe 3RRA · UniProt B2UCA8
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