Research workbench
Structure of mortalin-nbd with N6-propargyladenosine-5'-diphosphate
Analyse Structure of mortalin-nbd with N6-propargyladenosine-5'-diphosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P2U
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stress-70 protein, mitochondrial
- UniProt
- P38646
- Ligands
- NO7, MG, PO4
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stress-70 protein, mitochondrial | protein | 379 | 39% helix, 29% strand | P38646 |
Ligands and binding sites
- NO7 · 9-{5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-alpha-D-ribofuranosyl}-N-(prop-2-yn-1-yl)-9H-purin-6-amine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains 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 | 592 | 0.75 | 0.82 | 72 | NO7, PO4, MG |
Compared structures
- 6P2U · Structure of Mortalin-NBD with N6-propargyladenosine-5'-diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P38646 · AlphaFold monomer V2.0 prediction for stress-70 protein, mitochondrial (P38646) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P38646
- Elsewhere: RCSB PDB 6P2U · PDBe 6P2U · UniProt P38646
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