MolNFT v1 · #59692 · protein
Crystal structure of the conserved protein of unknown function RPA1785 from rhodopseudomonas palustris
3C5O · UPF0311 protein RPA1785: “Crystal structure of the conserved protein of unknown function RPA1785 from rhodopseudomonas palustris”. X-ray diffraction, 6 pockets (best druggability 0.84). MolNFT v1 #59692 on GenesisL1: 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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