Research workbench
Crystal structure of conserved uncharacterized protein from rhodopirellula baltica
Analyse Crystal structure of conserved uncharacterized protein from rhodopirellula… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B5M
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q7UTD8
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 194 | 34% helix, 29% strand | Q7UTD8 |
| B, D | Uncharacterized protein | protein | 195 | 34% helix, 30% strand | Q7UTD8 |
| C | Uncharacterized protein | protein | 192 | 33% helix, 29% strand | Q7UTD8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.70 | 0.76 | 70 | empty |
| 2 | 242 | 0.65 | 0.83 | 34 | empty |
| 3 | 316 | 0.65 | 0.81 | 40 | empty |
| 4 | 430 | 0.64 | 0.78 | 35 | SO4 |
| 5 | 387 | 0.62 | 0.78 | 41 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1529 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1527 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 310 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3B5M · Crystal structure of conserved uncharacterized protein from Rhodopirellula baltica · 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 Q7UTD8
- Elsewhere: RCSB PDB 3B5M · PDBe 3B5M · UniProt Q7UTD8
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