Research workbench
Crystal structure of E112A/H234A mutant of stationary phase survival protein (sure) from salmonella typhimurium co-crystallized with AMP
Analyse Crystal structure of E112A/H234A mutant of stationary phase survival protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XGB
- Type
- protein
- Length
- 1,028 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
- MG, PO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 29% 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, 3.6.1.11) | protein | 262 | 29% helix, 27% strand | P66881 |
| B | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 257 | 28% helix, 28% strand | P66881 |
| C | 5'/3'-nucleotidase sure (EC 3.1.3.5, 3.1.3.6, 3.6.1.11) | protein | 255 | 29% helix, 26% strand | P66881 |
| 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
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.84 | 0.85 | 101 | empty |
| 2 | 303 | 0.76 | 0.88 | 39 | MG, PO4 |
| 3 | 306 | 0.75 | 0.88 | 39 | PO4 |
| 4 | 557 | 0.72 | 0.81 | 58 | MG |
| 5 | 325 | 0.72 | 0.85 | 42 | PO4, MPD |
Interfaces
6 interfaces between chains.
- C–D · 3886 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3825 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 527 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XGB · Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (SurE) from… · the same entry in another collection · chain C against C, TM-score 1.00
- P66881 · AlphaFold monomer V2.0 prediction for 5'/3'-nucleotidase sure (P66881) · a predicted model of the same protein · chain D 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 4XGB · PDBe 4XGB · UniProt P66881
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