Research workbench
Crystal structure of a ribosome biogenesis GTP-binding protein (ysxc) from neisseria gonorrhoeae with bound GDP
Analyse Crystal structure of a ribosome biogenesis GTP-binding protein (ysxc) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UCV
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable GTP-binding protein engb
- UniProt
- B4RQ29
- Ligands
- GDP, CL, PO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable GTP-binding protein engb | protein | 187 | 41% helix, 24% strand | B4RQ29 |
| B | Probable GTP-binding protein engb | protein | 186 | 47% helix, 24% strand | B4RQ29 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- CL · Chloride ion · ion · chains A, B
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.53 | 0.77 | 26 | CL |
| 2 | 67 | 0.35 | 0.76 | 14 | empty |
| 3 | 50 | 0.35 | 0.80 | 17 | empty |
| 4 | 62 | 0.29 | 0.74 | 13 | ACT |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5UCV · Crystal Structure of a Ribosome Biogenesis GTP-binding protein (YsxC) from Neisseria… · the same entry in another collection · chain A against A, TM-score 1.00
- B4RQ29 · AlphaFold monomer V2.0 prediction for probable GTP-binding protein engb (B4RQ29) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 B4RQ29
- Elsewhere: RCSB PDB 5UCV · PDBe 5UCV · UniProt B4RQ29
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