MolNFT v1 · #92699 · protein
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)
4GGH · Putative uncharacterized protein: “Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to…”. X-ray diffraction, 2 ligands (MG, CL), 18 pockets (best druggability 0.86). MolNFT v1…
- 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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