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Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, hepes, and ethylene glycol bound (ordered loops, space group C2221)
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
- 4GGH
- Type
- protein
- Length
- 1,588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- D0X4R4
- Ligands
- MG, CL
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative uncharacterized protein | protein | 397 | 41% helix, 17% strand | D0X4R4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, C, D, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.86 | 0.90 | 87 | EDO |
| 2 | 379 | 0.85 | 0.94 | 48 | empty |
| 3 | 336 | 0.74 | 0.86 | 43 | EDO |
| 4 | 68 | 0.74 | 0.98 | 21 | empty |
| 5 | 591 | 0.71 | 0.79 | 48 | GOL, EPE |
Interfaces
5 interfaces between chains.
- C–D · 2505 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1293 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1291 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1261 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1249 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4GGH · Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692)… · the same entry in another collection · chain A against A, 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 A 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 D0X4R4
- Elsewhere: RCSB PDB 4GGH · PDBe 4GGH · UniProt D0X4R4
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