MolNFT v1 · #73948 · protein
Structure of the structure of the H13A mutant of YKR043C in complex with sedoheptulose-1,7-bisphosphate
3OI7 · Uncharacterized protein YKR043C: “Structure of the structure of the H13A mutant of YKR043C in complex with sedoheptulose-1,7-bisphosphate”. X-ray diffraction, 3 ligands (OI7, NA, MG), 12 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 3OI7
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein YKR043C
- EC
- 3.1.3.11
- UniProt
- P36136
- Ligands
- OI7, NA, MG
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized protein YKR043C (EC 3.1.3.11) | protein | 260 | 38% helix, 18% strand | P36136 |
Ligands and binding sites
- OI7 · 1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose · ligand · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.70 | 0.77 | 72 | OI7, MG, NA |
| 2 | 701 | 0.70 | 0.78 | 67 | OI7, MG, NA |
| 3 | 690 | 0.70 | 0.78 | 69 | OI7, NA |
| 4 | 678 | 0.70 | 0.77 | 72 | OI7, MG, EDO |
| 5 | 176 | 0.50 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1578 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1562 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3OI7 · Structure of the structure of the H13A mutant of Ykr043C in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P36136 · AlphaFold monomer V2.0 prediction for sedoheptulose 1,7-bisphosphatase (P36136) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P36136
- Elsewhere: RCSB PDB 3OI7 · PDBe 3OI7 · UniProt P36136
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