Research workbench
Crystal structure of the stationary phase survival protein sure from thermus thermophilus HB8 cocrystallized with manganese and AMP
Analyse Crystal structure of the stationary phase survival protein sure from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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