Research workbench
Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
Analyse Design of a binding scaffold based on variable lymphocyte receptors of jawless… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RFS
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Internalin B, repeat modules, variable lymphocyte receptor B
- UniProt
- D2P9A6, Q4G1L3
- Ligands
- MG
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Internalin B, repeat modules, variable lymphocyte receptor B | protein | 263 | 16% helix, 13% strand | D2P9A6, Q4G1L3 |
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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.55 | 0.76 | 30 | empty |
| 2 | 150 | 0.52 | 0.80 | 24 | MG |
| 3 | 230 | 0.51 | 0.76 | 28 | empty |
| 4 | 128 | 0.51 | 0.80 | 24 | MG |
Interfaces
1 interface between chains.
- A–B · 945 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3RFS · Design of a binding scaffold based on variable lymphocyte receptors of jawless… · 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
- Every structure of UniProt D2P9A6
- Every structure of UniProt Q4G1L3
- Elsewhere: RCSB PDB 3RFS · PDBe 3RFS · UniProt D2P9A6 · UniProt Q4G1L3
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