MolNFT v1 · #92436 · protein
Crystal structure of a hexonate dehydrogenase ortholog (target efi- 506402 from salmonella enterica, unliganded structure
4G81 · Putative hexonate dehydrogenase: “Crystal structure of a hexonate dehydrogenase ortholog (target efi- 506402 from salmonella enterica…”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.85). MolNFT v1 #92436 on…
- PDB
- 4G81
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hexonate dehydrogenase
- UniProt
- B5R540
- Ligands
- CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C | Putative hexonate dehydrogenase | protein | 253 | 52% helix, 15% strand | B5R540 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains D, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, C, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.85 | 0.90 | 51 | empty |
| 2 | 521 | 0.75 | 0.83 | 44 | GOL |
| 3 | 508 | 0.75 | 0.83 | 46 | EDO |
| 4 | 366 | 0.73 | 0.85 | 45 | EDO |
| 5 | 426 | 0.72 | 0.82 | 49 | empty |
Interfaces
6 interfaces between chains.
- D–B · 1573 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1571 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 1529 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1527 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 494 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4G81 · Crystal structure of a hexonate dehydrogenase ortholog (target efi-506402 from salmonella… · the same entry in another collection · chain D against D, TM-score 1.00
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 B5R540
- Elsewhere: RCSB PDB 4G81 · PDBe 4G81 · UniProt B5R540
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