Research workbench
Structure of GDP bound bipa
Analyse Structure of GDP bound bipa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A9X
- Type
- protein
- Length
- 556 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein
- UniProt
- B7MHF0
- Ligands
- GDP
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein | protein | 556 | 20% helix, 26% strand | B7MHF0 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.77 | 0.97 | 24 | empty |
| 2 | 91 | 0.77 | 0.98 | 24 | empty |
| 3 | 115 | 0.56 | 0.84 | 22 | empty |
| 4 | 201 | 0.55 | 0.79 | 26 | empty |
| 5 | 107 | 0.48 | 0.81 | 23 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5A9X · Structure of GDP bound BipA · 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
- Every structure of UniProt B7MHF0
- Elsewhere: RCSB PDB 5A9X · PDBe 5A9X · UniProt B7MHF0
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