Research workbench
Crystal structure of the conserved protein of unknown function RPA1785 from rhodopseudomonas palustris
Analyse Crystal structure of the conserved protein of unknown function RPA1785 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5O
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0311 protein RPA1785
- UniProt
- P61167
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0311 protein RPA1785 | protein | 149 | 8% helix, 59% strand | P61167 |
| B | UPF0311 protein RPA1785 | protein | 154 | 12% helix, 57% strand | P61167 |
| C | UPF0311 protein RPA1785 | protein | 149 | 9% helix, 57% strand | P61167 |
| D | UPF0311 protein RPA1785 | protein | 152 | 11% helix, 56% strand | P61167 |
Ligands and binding sites
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.84 | 0.87 | 105 | empty |
| 2 | 55 | 0.73 | 0.99 | 19 | empty |
| 3 | 57 | 0.72 | 0.98 | 22 | empty |
| 4 | 135 | 0.55 | 0.82 | 22 | empty |
| 5 | 79 | 0.31 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1232 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1218 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 976 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 959 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3C5O · Crystal structure of the conserved protein of unknown function RPA1785 from… · the same entry in another collection · chain D against D, TM-score 1.00
- P61167 · AlphaFold monomer V2.0 prediction for UPF0311 protein RPA1785 (P61167) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P61167
- Elsewhere: RCSB PDB 3C5O · PDBe 3C5O · UniProt P61167
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