Research workbench
Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, glycerol and dicarboxylates bound (mixed loops, space group I4122)
Analyse Crystal structure of an enolase family member from vibrio harveyi (efi-target… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GIS
- Type
- protein
- Length
- 805 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enolase
- UniProt
- D0X4R4
- Ligands
- MAE, MG, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enolase | protein | 405 | 41% helix, 17% strand | D0X4R4 |
| B | Enolase | protein | 400 | 43% helix, 17% strand | D0X4R4 |
Ligands and binding sites
- MAE · Maleic acid · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MLA · Malonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.71 | 0.79 | 57 | MLA, GOL |
| 2 | 473 | 0.70 | 0.80 | 45 | CL, GOL, MAE |
| 3 | 345 | 0.64 | 0.79 | 33 | empty |
| 4 | 359 | 0.63 | 0.79 | 33 | empty |
| 5 | 150 | 0.51 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2639 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4GIS · crystal structure of an enolase family member from vibrio harveyi (efi-target 501692)… · the same entry in another collection · chain B against B, TM-score 1.00
- D0X4R4 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member VME_00770… · 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 D0X4R4
- Elsewhere: RCSB PDB 4GIS · PDBe 4GIS · UniProt D0X4R4
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