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Crystal structure of a protein with unknown function from S23 ribosomal protein family (BT_0352) from bacteroides thetaiotaomicron vpi-5482 at 1.70 a resolution
Analyse Crystal structure of a protein with unknown function from S23 ribosomal protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RLD
- Type
- protein
- Length
- 558 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q8AAW0
- Ligands
- CA, CL
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 5 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 114 | 84% helix, 0% strand | Q8AAW0 |
| B | Uncharacterized protein | protein | 112 | 85% helix, 0% strand | Q8AAW0 |
| C | Uncharacterized protein | protein | 116 | 85% helix, 0% strand | Q8AAW0 |
| D | Uncharacterized protein | protein | 108 | 86% helix, 0% strand | Q8AAW0 |
| E | Uncharacterized protein | protein | 108 | 84% helix, 0% strand | Q8AAW0 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, C, B, E, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.51 | 0.76 | 39 | empty |
| 2 | 165 | 0.43 | 0.74 | 26 | EDO |
| 3 | 93 | 0.43 | 0.78 | 16 | empty |
| 4 | 96 | 0.39 | 0.77 | 14 | empty |
| 5 | 66 | 0.34 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 846 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 782 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 762 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 707 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 650 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2RLD · Crystal structure of a protein with unknown function from S23 ribosomal protein family… · 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 Q8AAW0
- Elsewhere: RCSB PDB 2RLD · PDBe 2RLD · UniProt Q8AAW0
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