MolNFT v1 · #68274 · protein
X-ray crystal structure of the mg-bound 3-keto-L-gulonate-6-phosphate decarboxylase from vibrio cholerae O1 biovar el tor str. N16961
3JR2 · Hexulose-6-phosphate synthase sgbh: “X-ray crystal structure of the mg-bound 3-keto-L-gulonate-6-phosphate decarboxylase from vibrio cholerae O1…”. X-ray diffraction, 2 ligands (MG, SO4), 6 pockets (best druggability 0.67). MolNFT…
- PDB
- 3JR2
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexulose-6-phosphate synthase sgbh
- UniProt
- Q9KMS8
- Ligands
- MG, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hexulose-6-phosphate synthase sgbh | protein | 213 | 52% helix, 21% strand | Q9KMS8 |
| B | Hexulose-6-phosphate synthase sgbh | protein | 213 | 48% helix, 21% strand | Q9KMS8 |
| C | Hexulose-6-phosphate synthase sgbh | protein | 214 | 50% helix, 21% strand | Q9KMS8 |
| D | Hexulose-6-phosphate synthase sgbh | protein | 212 | 50% helix, 21% strand | Q9KMS8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.67 | 0.77 | 61 | EDO, SO4, GOL |
| 2 | 532 | 0.67 | 0.77 | 58 | GOL, SO4, MG |
| 3 | 461 | 0.66 | 0.79 | 59 | EDO, SO4, MG |
| 4 | 479 | 0.65 | 0.78 | 53 | empty |
| 5 | 222 | 0.57 | 0.79 | 30 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1361 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1352 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3JR2 · X-ray crystal structure of the Mg-bound 3-keto-L-gulonate-6-phosphate decarboxylase from… · the same entry in another collection · chain A against A, 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 Q9KMS8
- Elsewhere: RCSB PDB 3JR2 · PDBe 3JR2 · UniProt Q9KMS8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.