Research workbench
Crystal structure of E112A mutant of stationary phase survival protein (sure) from salmonella typhimurium soaked with AMP
Analyse Crystal structure of E112A mutant of stationary phase survival protein (sure)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJ7
- Type
- protein
- Length
- 1,030 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, 3.6.1.11
- UniProt
- P66881
- Ligands
- ADN, ADE, MG, PO4
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 263 | 29% helix, 25% strand | P66881 |
| B | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 259 | 29% helix, 26% strand | P66881 |
| C, D | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 254 | 30% helix, 27% strand | P66881 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B, C, D
- ADE · Adenine · ligand · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.86 | 0.88 | 103 | empty |
| 2 | 246 | 0.76 | 0.90 | 38 | PO4, ADN, GOL |
| 3 | 310 | 0.72 | 0.85 | 41 | PO4, GOL |
| 4 | 224 | 0.72 | 0.88 | 37 | PO4, ADN |
| 5 | 281 | 0.70 | 0.85 | 37 | PO4, ADE |
Interfaces
6 interfaces between chains.
- C–D · 3859 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 3843 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 490 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4XJ7 · Crystal Structure of E112A Mutant of Stationary Phase Survival Protein (SurE) from… · 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 0.98
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 4XJ7 · PDBe 4XJ7 · UniProt P66881
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