Research workbench
Crystal structure of a putative multiple antibiotic-resistance repressor (SSU05_1136) from streptococcus suis 89/1591 at 2.20 a resolution
Analyse Crystal structure of a putative multiple antibiotic-resistance repressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BDD
- Type
- protein
- Length
- 545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein marr
- UniProt
- Q2ZYK0
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Regulatory protein marr | protein | 140 | 69% helix, 8% strand | Q2ZYK0 |
| B | Regulatory protein marr | protein | 133 | 72% helix, 7% strand | Q2ZYK0 |
| D | Regulatory protein marr | protein | 132 | 73% helix, 7% strand | Q2ZYK0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, D, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.69 | 0.78 | 55 | PO4 |
| 2 | 565 | 0.63 | 0.75 | 56 | GOL |
| 3 | 131 | 0.42 | 0.75 | 19 | empty |
| 4 | 129 | 0.40 | 0.75 | 21 | empty |
| 5 | 98 | 0.37 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2970 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2943 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 293 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3BDD · Crystal structure of a putative multiple antibiotic-resistance repressor (SSU05_1136)… · 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 Q2ZYK0
- Elsewhere: RCSB PDB 3BDD · PDBe 3BDD · UniProt Q2ZYK0
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