Research workbench
Crystal structure of red abalone verl repeat 2 with linker at 2.5 a resolution
Analyse Crystal structure of red abalone verl repeat 2 with linker at 2.5 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MR2
- Type
- protein
- Length
- 318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitelline envelope sperm lysin receptor
- UniProt
- Q8WR62
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitelline envelope sperm lysin receptor | protein | 107 | 0% helix, 57% strand | Q8WR62 |
| B | Vitelline envelope sperm lysin receptor | protein | 106 | 0% helix, 58% strand | Q8WR62 |
| C | Vitelline envelope sperm lysin receptor | protein | 105 | 0% helix, 57% strand | Q8WR62 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.58 | 0.83 | 18 | empty |
| 2 | 234 | 0.47 | 0.73 | 28 | empty |
| 3 | 115 | 0.40 | 0.75 | 25 | empty |
| 4 | 101 | 0.39 | 0.76 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 802 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 270 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5MR2 · Crystal structure of red abalone VERL repeat 2 with linker at 2.5 A resolution · 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 Q8WR62
- Elsewhere: RCSB PDB 5MR2 · PDBe 5MR2 · UniProt Q8WR62
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