Research workbench
Crystal structure of 2,3-diketo-5-methylthiopentyl-1- phosphate enolase from bacillus subtilis
Analyse Crystal structure of 2,3-diketo-5-methylthiopentyl-1- phosphate enolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZVI
- Type
- protein
- Length
- 1,564 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
- EC
- 5.3.2.-
- UniProt
- O31666
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 395 | 47% helix, 16% strand | O31666 |
| B | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 396 | 45% helix, 16% strand | O31666 |
| C | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 385 | 43% helix, 17% strand | O31666 |
| D | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (EC 5.3.2.-) | protein | 388 | 46% helix, 16% strand | O31666 |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.82 | 0.97 | 31 | empty |
| 2 | 141 | 0.81 | 0.97 | 30 | empty |
| 3 | 1051 | 0.79 | 0.81 | 104 | empty |
| 4 | 585 | 0.73 | 0.81 | 56 | empty |
| 5 | 645 | 0.72 | 0.79 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2486 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2371 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 319 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2ZVI · Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus… · the same entry in another collection · chain D against D, TM-score 1.00
- O31666 · AlphaFold monomer V2.0 prediction for 2,3-diketo-5-methylthiopentyl-1-phosphate enolase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O31666
- Elsewhere: RCSB PDB 2ZVI · PDBe 2ZVI · UniProt O31666
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