Research workbench
Stationary phase survival protein E (sure) from xylella fastidiosa - xfsure-tb (tetramer bigger).
Analyse Stationary phase survival protein E (sure) from xylella fastidiosa - xfsure-tb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KSR
- Type
- protein
- Length
- 1,026 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
- Q9PF20
- Ligands
- MN, IOD, CL
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 255 | 31% helix, 27% strand | Q9PF20 |
| B | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 254 | 31% helix, 27% strand | Q9PF20 |
| C | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 258 | 31% helix, 28% strand | Q9PF20 |
| D | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 259 | 32% helix, 25% strand | Q9PF20 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- IOD · Iodide ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.73 | 0.81 | 66 | CL |
| 2 | 578 | 0.72 | 0.80 | 75 | MN, CL |
| 3 | 459 | 0.69 | 0.80 | 55 | MN, CL |
| 4 | 553 | 0.68 | 0.79 | 68 | MN, CL |
| 5 | 145 | 0.53 | 0.80 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4067 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3943 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 647 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 386 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KSR · Stationary phase survival protein E (SurE) from Xylella fastidiosa - XFSurE-TB (Tetramer… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9PF20 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase sure (Q9PF20) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q9PF20
- Elsewhere: RCSB PDB 5KSR · PDBe 5KSR · UniProt Q9PF20
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