MolNFT v1 · #35274 · protein
Crystal structure of E37A mutant of the stationary phase survival protein sure from thermus thermophilus HB8 cocrystallized with manganese and AMP
2E6H · 5'-nucleotidase sure: “Crystal structure of E37A mutant of the stationary phase survival protein sure from thermus thermophilus HB8…”. X-ray diffraction, 2 ligands (MN, SO4), 9 pockets (best druggability 0.77). MolNFT v1 #35274 on…
- PDB
- 2E6H
- Type
- protein
- Length
- 932 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase sure
- EC
- 3.1.3.5
- UniProt
- Q53W92
- Ligands
- MN, SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 236 | 25% helix, 29% strand | Q53W92 |
| B | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 231 | 28% helix, 29% strand | Q53W92 |
| C | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 231 | 26% helix, 30% strand | Q53W92 |
| D | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 234 | 27% helix, 30% strand | Q53W92 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.77 | 0.81 | 70 | empty |
| 2 | 132 | 0.59 | 0.84 | 28 | empty |
| 3 | 120 | 0.50 | 0.80 | 24 | SO4 |
| 4 | 211 | 0.49 | 0.75 | 31 | GOL, SO4 |
| 5 | 55 | 0.48 | 0.85 | 14 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 3312 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2905 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 736 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 499 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 429 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2E6H · Crystal structure of E37A mutant of the stationary phase survival protein SurE from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q53W92 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase sure (Q53W92) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q53W92
- Elsewhere: RCSB PDB 2E6H · PDBe 2E6H · UniProt Q53W92
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