MolNFT v1 · #122849 · protein
Torsinadeltae-LULL1 complex, H. sapiens, bound to vhh-BS2
5J1T · Torsin-1A: “Torsinadeltae-LULL1 complex, H. sapiens, bound to vhh-BS2”. X-ray diffraction, 3 ligands (ATP, MG, CL), 7 pockets (best druggability 0.74). MolNFT v1 #122849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5J1T
- Type
- protein
- Length
- 633 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Torsin-1A; Torsin-1A-interacting protein 2; Vhh domain bs-2
- EC
- 3.6.4.-
- UniProt
- O14656, Q8NFQ8
- Ligands
- ATP, MG, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Torsin-1A (EC 3.6.4.-) | protein | 277 | 49% helix, 13% strand | O14656 |
| B | Torsin-1A-interacting protein 2 | protein | 235 | 49% helix, 11% strand | Q8NFQ8 |
| C | Vhh domain bs-2 | protein | 121 | 5% helix, 52% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · chains A, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.74 | 0.82 | 51 | ATP, MG |
| 2 | 296 | 0.67 | 0.82 | 36 | empty |
| 3 | 58 | 0.54 | 0.88 | 18 | empty |
| 4 | 218 | 0.50 | 0.76 | 25 | empty |
| 5 | 128 | 0.46 | 0.78 | 21 | BTB |
Interfaces
3 interfaces between chains.
- A–B · 1672 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 648 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5J1T · TorsinAdeltaE-LULL1 complex, H. sapiens, bound to VHH-BS2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NFQ8 · AlphaFold monomer V2.0 prediction for torsin-1A-interacting protein 2 (Q8NFQ8) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O14656 · AlphaFold monomer V2.0 prediction for torsin-1A (O14656) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O14656
- Every structure of UniProt Q8NFQ8
- Elsewhere: RCSB PDB 5J1T · PDBe 5J1T · UniProt O14656 · UniProt Q8NFQ8
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