MolNFT v1 · #22662 · protein
Ligand induced conformational shift in the N-terminal domain of GRP94, open conformation ADP-complex
1TC6 · Endoplasmin: “Ligand induced conformational shift in the N-terminal domain of GRP94, open conformation ADP-complex”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.53). MolNFT v1 #22662 on GenesisL1: 3D…
- PDB
- 1TC6
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmin
- UniProt
- P41148
- Ligands
- ADP, MG
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmin | protein | 222 | 43% helix, 24% strand | P41148 |
| B | Endoplasmin | protein | 194 | 36% helix, 27% strand | P41148 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.53 | 0.79 | 26 | ADP |
| 2 | 122 | 0.52 | 0.81 | 19 | ADP |
| 3 | 58 | 0.48 | 0.84 | 14 | empty |
| 4 | 81 | 0.33 | 0.74 | 21 | empty |
| 5 | 62 | 0.31 | 0.76 | 21 | PG4 |
Interfaces
1 interface between chains.
- A–B · 794 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1TC6 · Ligand Induced Conformational Shift in the N-terminal Domain of GRP94, Open Conformation… · the same entry in another collection · chain A against A, TM-score 1.00
- P41148 · AlphaFold monomer V2.0 prediction for endoplasmin (P41148) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 P41148
- Elsewhere: RCSB PDB 1TC6 · PDBe 1TC6 · UniProt P41148
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