Research workbench
Camelid vhh domains in complex with porcine pancreatic alpha-amylase
Analyse Camelid vhh domains in complex with porcine pancreatic alpha-amylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KXV
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, pancreatic; Camelid vhh domain CAB10
- EC
- 3.2.1.1
- UniProt
- P00690
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-amylase, pancreatic (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P00690 |
| C | Camelid vhh domain CAB10 | protein | 119 | 5% helix, 50% strand | — |
| D | Camelid vhh domain CAB10 | protein | 121 | 5% helix, 50% strand | — |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.68 | 0.78 | 81 | empty |
| 2 | 300 | 0.61 | 0.79 | 30 | empty |
| 3 | 302 | 0.59 | 0.78 | 28 | empty |
| 4 | 130 | 0.49 | 0.79 | 24 | empty |
| 5 | 119 | 0.47 | 0.79 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–D · 924 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 867 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 252 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1KXV · Camelid VHH Domains in Complex with Porcine Pancreatic alpha-Amylase · the same entry in another collection · chain A against A, TM-score 1.00
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · a predicted model of the same protein · 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 P00690
- Elsewhere: RCSB PDB 1KXV · PDBe 1KXV · UniProt P00690
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