MolNFT v1 · #128944 · protein
X-ray crystal structure of rapz from escherichia COLI (P32 space group)
5O5O · RNase adapter protein rapz: “X-ray crystal structure of rapz from escherichia COLI (P32 space group)”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.75). MolNFT v1 #128944 on GenesisL1: 3D structure, binding…
- PDB
- 5O5O
- Type
- protein
- Length
- 1,077 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 0.75
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNase adapter protein rapz | protein | 269 | 45% helix, 19% strand | P0A894 |
| B | RNase adapter protein rapz | protein | 261 | 45% helix, 20% strand | P0A894 |
| C | RNase adapter protein rapz | protein | 276 | 43% helix, 19% strand | P0A894 |
| D | RNase adapter protein rapz | protein | 271 | 43% helix, 19% strand | P0A894 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.75 | 0.78 | 81 | SO4 |
| 2 | 1010 | 0.75 | 0.78 | 103 | SO4 |
| 3 | 216 | 0.65 | 0.83 | 43 | empty |
| 4 | 333 | 0.64 | 0.79 | 32 | SO4 |
| 5 | 240 | 0.62 | 0.81 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1464 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1432 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1415 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1249 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 110 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O5O · X-ray crystal structure of RapZ from Escherichia coli (P32 space group) · the same entry in another collection · chain D against D, 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 0.57
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 5O5O · PDBe 5O5O · UniProt P0A894
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