MolNFT v1 · #135989 · protein
Crystal structure of variable lymphocyte receptor (vlr) RBC36 (apo)
5UFD: “Crystal structure of variable lymphocyte receptor (vlr) RBC36 (apo)”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.43). MolNFT v1 #135989 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UFD
- Type
- protein
- Length
- 457 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RBC36
- Ligands
- MG
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RBC36 | protein | 229 | 12% helix, 16% strand | — |
| B | RBC36 | protein | 228 | 12% helix, 16% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.43 | 0.73 | 29 | empty |
| 2 | 72 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5UFD · Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 (Apo) · the same entry in another collection · chain A against A, 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 5UFD · PDBe 5UFD
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