MolNFT v1 · #106429 · protein
Crystal structure of C2 form of E112A mutant of stationary phase survival protein (sure) from salmonella typhimurium
4RYU · 5'/3'-nucleotidase sure: “Crystal structure of C2 form of E112A mutant of stationary phase survival protein (sure) from salmonella…”. X-ray diffraction, 2 ligands (MG, PO4), 16 pockets (best druggability 0.86). MolNFT v1 #106429 on…
- 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
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