MolNFT v1 · #61125 · protein
Crystal structure of the RPA0582- protein of unknown function from rhodopseudomonas palustris- a structural genomics target
3DCA: “Crystal structure of the RPA0582- protein of unknown function from rhodopseudomonas palustris- a structural…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.65). MolNFT v1 #61125 on GenesisL1: 3D structure…
- PDB
- 3DCA
- Type
- protein
- Length
- 520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RPA0582
- UniProt
- Q6NC90
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RPA0582 | protein | 130 | 38% helix, 32% strand | Q6NC90 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, 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 | 262 | 0.65 | 0.82 | 36 | SO4 |
| 2 | 241 | 0.63 | 0.81 | 34 | SO4 |
| 3 | 268 | 0.63 | 0.80 | 32 | SO4 |
| 4 | 254 | 0.61 | 0.79 | 32 | SO4 |
| 5 | 125 | 0.40 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1979 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1973 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3DCA · Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas… · 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 Q6NC90
- Elsewhere: RCSB PDB 3DCA · PDBe 3DCA · UniProt Q6NC90
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