Research workbench
Pyrococcus horikoshii NOP5 RNA binding domain from a twinned crystal form
Analyse Pyrococcus horikoshii NOP5 RNA binding domain from a twinned crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GQX
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NOP5P protein
- UniProt
- O57810
- Ligands
- IOD
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | NOP5P protein | protein | 113 | 69% helix, 0% strand | O57810 |
| A | NOP5P protein | protein | 116 | 67% helix, 0% strand | O57810 |
Ligands and binding sites
- IOD · Iodide ion · ion · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.58 | 0.77 | 36 | IOD |
Interfaces
1 interface between chains.
- B–A · 411 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3GQX · Pyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crystal form · the same entry in another collection · chain B against B, 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 O57810
- Elsewhere: RCSB PDB 3GQX · PDBe 3GQX · UniProt O57810
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