MolNFT v1 · #23113 · protein
Ovine recombinant PRP(114-234), vrq variant in complex with the Fab of the VRQ14 antibody
1TQB · Prion protein: “Ovine recombinant PRP(114-234), vrq variant in complex with the Fab of the VRQ14 antibody”. X-ray diffraction, 5 pockets (best druggability 0.51). MolNFT v1 #23113 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1TQB
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prion protein; VRQ14 Fab heavy chain; VRQ14 Fab light chain
- UniProt
- P23907
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prion protein | protein | 102 | 61% helix, 4% strand | P23907 |
| B | VRQ14 Fab heavy chain | protein | 212 | 10% helix, 50% strand | — |
| C | VRQ14 Fab light chain | protein | 219 | 6% helix, 51% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.51 | 0.76 | 30 | empty |
| 2 | 92 | 0.45 | 0.80 | 21 | empty |
| 3 | 239 | 0.44 | 0.72 | 38 | empty |
| 4 | 79 | 0.30 | 0.73 | 19 | empty |
| 5 | 63 | 0.30 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1661 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1TQB · Ovine recombinant PrP(114-234), VRQ variant in complex with the Fab of the VRQ14 antibody · the same entry in another collection · chain A against A, TM-score 1.00
- P23907 · AlphaFold monomer V2.0 prediction for major prion protein (P23907) · 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 P23907
- Elsewhere: RCSB PDB 1TQB · PDBe 1TQB · UniProt P23907
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