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Crystal structure of ATPase domain of malaria GRP78 with ADP bound
Analyse Crystal structure of ATPase domain of malaria GRP78 with ADP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UMB
- Type
- protein
- Length
- 1,510 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone dnak
- UniProt
- W7JXN5
- Ligands
- ADP, MG, PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chaperone dnak | protein | 378 | 40% helix, 29% strand | W7JXN5 |
| C | Chaperone dnak | protein | 377 | 41% helix, 28% strand | W7JXN5 |
| D | Chaperone dnak | protein | 377 | 42% helix, 29% strand | W7JXN5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.80 | 0.82 | 88 | MG, PO4, ADP |
| 2 | 846 | 0.79 | 0.82 | 86 | MG, PO4, ADP |
| 3 | 660 | 0.77 | 0.83 | 72 | MG, PO4, ADP |
| 4 | 413 | 0.76 | 0.85 | 53 | MG, PO4, ADP |
| 5 | 813 | 0.73 | 0.78 | 61 | empty |
Interfaces
2 interfaces between chains.
- B–C · 649 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 467 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5UMB · Crystal structure of ATPase domain of Malaria GRP78 with ADP bound · 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 W7JXN5
- Elsewhere: RCSB PDB 5UMB · PDBe 5UMB · UniProt W7JXN5
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