Research workbench
Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution
Analyse Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IIC
- Type
- protein
- Length
- 939 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Escherichia coli; Haliotis rufescens
- Molecule
- Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor
- UniProt
- P0AEX9, Q8WR62
- Ligands
- GLC, NAG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor | protein | 472 | 36% helix, 29% strand | P0AEX9, Q8WR62 |
| B | Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor | protein | 467 | 37% helix, 28% strand | P0AEX9, Q8WR62 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.86 | 0.87 | 121 | empty |
| 2 | 712 | 0.77 | 0.82 | 58 | GLC, NAG |
| 3 | 800 | 0.76 | 0.80 | 89 | empty |
| 4 | 265 | 0.73 | 0.86 | 26 | GLC |
| 5 | 88 | 0.69 | 0.93 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1742 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5IIC · Crystal structure of red abalone verl repeat 3 at 2.9 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 P0AEX9
- Every structure of UniProt Q8WR62
- Elsewhere: RCSB PDB 5IIC · PDBe 5IIC · UniProt P0AEX9 · UniProt Q8WR62
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.