MolNFT v1 · #138466 · protein
Crystal structure of an anti-idiotype vlr
5WK4 · Variable lymphocyte receptor 39: “Crystal structure of an anti-idiotype vlr”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.79). MolNFT v1 #138466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WK4
- Type
- protein
- Length
- 1,148 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable lymphocyte receptor 39
- Ligands
- MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B, C | Variable lymphocyte receptor 39 | protein | 192 | 14% helix, 15% strand | — |
| A | Variable lymphocyte receptor 39 | protein | 190 | 13% helix, 15% strand | — |
| E, F | Variable lymphocyte receptor 39 | protein | 191 | 13% helix, 15% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains D, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.79 | 0.83 | 107 | MG |
| 2 | 394 | 0.70 | 0.82 | 37 | empty |
| 3 | 244 | 0.50 | 0.75 | 26 | empty |
| 4 | 198 | 0.48 | 0.75 | 26 | empty |
| 5 | 177 | 0.43 | 0.74 | 25 | empty |
Interfaces
9 interfaces between chains.
- B–C · 663 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 614 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 494 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 363 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 353 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 5WK4 · Crystal structure of an anti-idiotype VLR · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 5WK4 · PDBe 5WK4
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