Research workbench
Crystal structure of nysgrc enolase target 200555, a putative dipeptide epimerase from francisella philomiragia : tartrate bound, no mg
Analyse Crystal structure of nysgrc enolase target 200555, a putative dipeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R0K
- Type
- protein
- Length
- 719 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enzyme of enolase superfamily
- UniProt
- B0TZW0
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enzyme of enolase superfamily | protein | 355 | 45% helix, 21% strand | B0TZW0 |
| B | Enzyme of enolase superfamily | protein | 364 | 41% helix, 24% strand | B0TZW0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.83 | 0.84 | 83 | GOL |
| 2 | 52 | 0.69 | 0.97 | 20 | SO4 |
| 3 | 142 | 0.56 | 0.83 | 30 | TAR |
| 4 | 151 | 0.51 | 0.79 | 22 | GOL |
| 5 | 131 | 0.50 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1126 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3R0K · Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from… · the same entry in another collection · chain A against A, TM-score 1.00
- B0TZW0 · AlphaFold monomer V2.0 prediction for L-amino acid-D/L-glu epimerase (B0TZW0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 B0TZW0
- Elsewhere: RCSB PDB 3R0K · PDBe 3R0K · UniProt B0TZW0
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