Research workbench
PAB0955 crystal structure : a GTPase in GDP and mg bound form from pyrococcus abyssi
Analyse PAB0955 crystal structure : a GTPase in GDP and mg bound form from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YRB
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP(GTP)BINDING protein
- Ligands
- GDP, MG
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP(GTP)BINDING protein | protein | 259 | 53% helix, 12% strand | — |
| B | ATP(GTP)BINDING protein | protein | 260 | 54% helix, 13% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.65 | 0.79 | 54 | MG, GDP |
| 2 | 175 | 0.58 | 0.81 | 30 | empty |
| 3 | 260 | 0.53 | 0.75 | 33 | empty |
| 4 | 209 | 0.53 | 0.77 | 34 | MG, GDP |
| 5 | 68 | 0.33 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2225 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1YRB · PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi · 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
- Elsewhere: RCSB PDB 1YRB · PDBe 1YRB
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.