MolNFT v1 · #35269 · protein
Crystal structure of the stationary phase survival protein sure from thermus thermophilus HB8 cocrystallized with manganese and AMP
2E6C · 5'-nucleotidase sure: “Crystal structure of the stationary phase survival protein sure from thermus thermophilus HB8 cocrystallized…”. X-ray diffraction, 2 ligands (MN, SO4), 8 pockets (best druggability 0.83). MolNFT v1 #35269 on…
- PDB
- 2E6C
- Type
- protein
- Length
- 952 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
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 243 | 24% helix, 29% strand | Q53W92 |
| B | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 237 | 25% helix, 29% strand | Q53W92 |
| C | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 238 | 25% helix, 29% strand | Q53W92 |
| D | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 234 | 26% helix, 29% strand | Q53W92 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.83 | 0.85 | 101 | empty |
| 2 | 266 | 0.66 | 0.83 | 37 | empty |
| 3 | 318 | 0.55 | 0.75 | 32 | empty |
| 4 | 78 | 0.51 | 0.84 | 18 | empty |
| 5 | 186 | 0.49 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3289 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 3025 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1121 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 481 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2E6C · Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus… · 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 0.93
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 2E6C · PDBe 2E6C · UniProt Q53W92
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