Research workbench
Crystal structure of rpfb catalytic domain in complex with benzamidine
Analyse Crystal structure of rpfb catalytic domain in complex with benzamidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EMN
- Type
- protein
- Length
- 322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable resuscitation-promoting factor rpfb
- UniProt
- O05594
- Ligands
- BEN, SO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable resuscitation-promoting factor rpfb | protein | 81 | 54% helix, 2% strand | O05594 |
| B, D | Probable resuscitation-promoting factor rpfb | protein | 80 | 53% helix, 3% strand | O05594 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.61 | 0.78 | 42 | BEN, SO4 |
| 2 | 210 | 0.51 | 0.76 | 36 | empty |
| 3 | 75 | 0.36 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 312 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 288 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 219 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 89 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4EMN · Crystal structure of RpfB catalytic domain in complex with benzamidine · 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 O05594
- Elsewhere: RCSB PDB 4EMN · PDBe 4EMN · UniProt O05594
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