Research workbench
Structural and functional insights into survival endonuclease, an important virulence factor of brucella abortus
Analyse Structural and functional insights into survival endonuclease, an important… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZG5
- Type
- protein
- Length
- 995 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
- B2S5B9
- Ligands
- MG
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 252 | 28% helix, 30% strand | B2S5B9 |
| A | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 247 | 28% helix, 30% strand | B2S5B9 |
| C | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 249 | 30% helix, 31% strand | B2S5B9 |
| G | 5'-nucleotidase sure (EC 3.1.3.5) | protein | 247 | 28% helix, 29% strand | B2S5B9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains D, A, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.74 | 0.84 | 42 | empty |
| 2 | 408 | 0.73 | 0.84 | 47 | empty |
| 3 | 369 | 0.73 | 0.84 | 44 | empty |
| 4 | 382 | 0.73 | 0.84 | 41 | empty |
| 5 | 462 | 0.72 | 0.82 | 41 | empty |
Interfaces
6 interfaces between chains.
- D–C · 3089 Ų buried · 38 hydrogen bonds · protein-protein
- A–G · 3061 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 693 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 318 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZG5 · Structural and functional insights into Survival endonuclease, an important virulence… · the same entry in another collection · chain G against G, TM-score 1.00
- B2S5B9 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase sure (B2S5B9) · 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 B2S5B9
- Elsewhere: RCSB PDB 4ZG5 · PDBe 4ZG5 · UniProt B2S5B9
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