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Crystal structure of lamprey variable lymphocyte receptor 2913 ectodomain
Analyse Crystal structure of lamprey variable lymphocyte receptor 2913 ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R9U
- Type
- protein
- Length
- 696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Variable lymphocyte receptor
- UniProt
- Q6E4B4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Variable lymphocyte receptor | protein | 174 | 14% helix, 17% strand | Q6E4B4 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.79 | 0.83 | 90 | empty |
| 2 | 123 | 0.55 | 0.83 | 27 | empty |
| 3 | 185 | 0.53 | 0.79 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 552 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 547 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 187 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2R9U · Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain · 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 Q6E4B4
- Elsewhere: RCSB PDB 2R9U · PDBe 2R9U · UniProt Q6E4B4
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