Research workbench
Crystal structure of nysgrc enolase target 200555, a putative dipeptide epimerase from francisella philomiragia : mg complex
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
- 3R10
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enzyme of enolase superfamily
- UniProt
- B0TZW0
- Ligands
- MG, SO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enzyme of enolase superfamily | protein | 362 | 43% helix, 23% strand | B0TZW0 |
| B | Enzyme of enolase superfamily | protein | 364 | 40% helix, 24% strand | B0TZW0 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.86 | 0.87 | 121 | SO4, GOL |
| 2 | 192 | 0.71 | 0.88 | 37 | SO4, GOL |
| 3 | 113 | 0.51 | 0.81 | 17 | empty |
| 4 | 87 | 0.47 | 0.81 | 18 | GOL |
| 5 | 78 | 0.41 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1212 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3R10 · 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 B 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 3R10 · PDBe 3R10 · UniProt B0TZW0
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