Research workbench
X-ray crystal structure of rapz from escherichia COLI (P3221 space group)
Analyse X-ray crystal structure of rapz from escherichia COLI (P3221 space group) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O5Q
- Type
- protein
- Length
- 1,067 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNase adapter protein rapz
- UniProt
- P0A894
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNase adapter protein rapz | protein | 265 | 42% helix, 21% strand | P0A894 |
| B | RNase adapter protein rapz | protein | 272 | 43% helix, 17% strand | P0A894 |
| D | RNase adapter protein rapz | protein | 276 | 42% helix, 20% strand | P0A894 |
| C | RNase adapter protein rapz | protein | 254 | 43% helix, 19% strand | P0A894 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.76 | 0.79 | 78 | SO4 |
| 2 | 218 | 0.71 | 0.87 | 36 | empty |
| 3 | 544 | 0.68 | 0.78 | 60 | SO4 |
| 4 | 379 | 0.66 | 0.79 | 31 | empty |
| 5 | 535 | 0.63 | 0.75 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1505 Ų buried · 23 hydrogen bonds · protein-protein
- D–C · 1451 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1437 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1390 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 138 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5O5Q · X-ray crystal structure of RapZ from Escherichia coli (P3221 space group) · the same entry in another collection · chain C against C, TM-score 1.00
- P0A894 · AlphaFold monomer V2.0 prediction for RNase adapter protein rapz (P0A894) · a predicted model of the same protein · chain A against A, TM-score 0.58
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 P0A894
- Elsewhere: RCSB PDB 5O5Q · PDBe 5O5Q · UniProt P0A894
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