Research workbench
Structure of the barley limit dextrinase-limit dextrinase inhibitor complex
Analyse Structure of the barley limit dextrinase-limit dextrinase inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CVW
- Type
- protein
- Length
- 1,948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Limit dextrinase; Limit dextrinase inhibitor
- EC
- 3.2.1.41
- UniProt
- O48541, Q2V8X0
- Ligands
- CA
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limit dextrinase (EC 3.2.1.41) | protein | 874 | 30% helix, 23% strand | O48541 |
| B | Limit dextrinase (EC 3.2.1.41) | protein | 871 | 29% helix, 22% strand | O48541 |
| C | Limit dextrinase inhibitor | protein | 101 | 48% helix, 6% strand | Q2V8X0 |
| D | Limit dextrinase inhibitor | protein | 102 | 45% helix, 6% strand | Q2V8X0 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.83 | 0.86 | 98 | empty |
| 2 | 947 | 0.83 | 0.84 | 82 | empty |
| 3 | 776 | 0.81 | 0.84 | 104 | empty |
| 4 | 609 | 0.76 | 0.83 | 72 | empty |
| 5 | 169 | 0.69 | 0.88 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1408 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1338 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4CVW · Structure of the barley limit dextrinase-limit dextrinase inhibitor complex · 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 O48541
- Every structure of UniProt Q2V8X0
- Elsewhere: RCSB PDB 4CVW · PDBe 4CVW · UniProt O48541 · UniProt Q2V8X0
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