MolNFT v1 · #104648 · protein
Crystal structure of nuca from streptococcus agalactiae with magnesium ion bound
4QH0 · DNA-entry nuclease (competence-specific nuclease): “Crystal structure of nuca from streptococcus agalactiae with magnesium ion bound”. X-ray diffraction, 3 ligands (MG, SO4, CL), 9 pockets (best druggability 0.82). MolNFT v1 #104648…
- PDB
- 4QH0
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-entry nuclease (competence-specific nuclease)
- UniProt
- R5A2Y6
- Ligands
- MG, SO4, CL
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA-entry nuclease (competence-specific nuclease) | protein | 219 | 18% helix, 29% strand | R5A2Y6 |
| C | DNA-entry nuclease (competence-specific nuclease) | protein | 217 | 18% helix, 29% strand | R5A2Y6 |
| D | DNA-entry nuclease (competence-specific nuclease) | protein | 215 | 18% helix, 31% strand | R5A2Y6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 23 copies · chains A, B, D, C
- CL · Chloride ion · ion · 6 copies · chains A, D, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.82 | 0.84 | 98 | SO4 |
| 2 | 188 | 0.49 | 0.76 | 41 | MG, SO4, CL |
| 3 | 110 | 0.45 | 0.79 | 23 | MG |
| 4 | 95 | 0.37 | 0.75 | 23 | empty |
| 5 | 97 | 0.36 | 0.75 | 17 | MG, SO4 |
Interfaces
5 interfaces between chains.
- B–D · 581 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 551 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 364 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QH0 · Crystal structure of NucA from Streptococcus agalactiae with magnesium ion bound · the same entry in another collection · chain A against A, TM-score 1.00
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 R5A2Y6
- Elsewhere: RCSB PDB 4QH0 · PDBe 4QH0 · UniProt R5A2Y6
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