Research workbench
Crystal structure of C2 form of E112A mutant of stationary phase survival protein (sure) from salmonella typhimurium
Analyse Crystal structure of C2 form of E112A mutant of stationary phase survival… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RYU
- Type
- protein
- Length
- 1,021 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'/3'-nucleotidase sure
- EC
- 3.1.3.5, 3.1.3.6
- UniProt
- P66881
- Ligands
- MG, PO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6) | protein | 258 | 29% helix, 27% strand | P66881 |
| B | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6) | protein | 255 | 30% helix, 27% strand | P66881 |
| C, D | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6) | protein | 254 | 30% helix, 28% strand | P66881 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains B, C, D, A
- GOL · Glycerol · additive · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.86 | 0.88 | 81 | empty |
| 2 | 326 | 0.76 | 0.88 | 36 | PO4, MPD |
| 3 | 224 | 0.75 | 0.89 | 34 | MPD, GOL, PO4 |
| 4 | 325 | 0.73 | 0.85 | 40 | PO4, GOL, MPD |
| 5 | 343 | 0.73 | 0.85 | 39 | PO4, GOL, MPD |
Interfaces
6 interfaces between chains.
- C–D · 3884 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3880 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 497 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4RYU · Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE)… · the same entry in another collection · chain A against A, TM-score 1.00
- P66881 · AlphaFold monomer V2.0 prediction for 5'/3'-nucleotidase sure (P66881) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P66881
- Elsewhere: RCSB PDB 4RYU · PDBe 4RYU · UniProt P66881
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.