Research workbench
Camelid vhh domain in complex with porcine pancreatic alpha-amylase
Analyse Camelid vhh domain 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
- 1KXQ
- Type
- protein
- Length
- 2,464 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, pancreatic; Antibody vhh fragment CABAMD9
- EC
- 3.2.1.1
- UniProt
- P00690
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha-amylase, pancreatic (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P00690 |
| E, F, G, H | Antibody vhh fragment CABAMD9 | protein | 120 | 5% helix, 49% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.79 | 0.86 | 41 | empty |
| 2 | 1020 | 0.79 | 0.80 | 79 | empty |
| 3 | 943 | 0.78 | 0.80 | 84 | empty |
| 4 | 451 | 0.78 | 0.86 | 38 | empty |
| 5 | 413 | 0.77 | 0.86 | 40 | empty |
Interfaces
9 interfaces between chains.
- A–H · 1137 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1132 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 1123 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1087 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 643 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 1KXQ · Camelid VHH Domain in Complex with Porcine Pancreatic alpha-Amylase · the same entry in another collection · chain E against E, TM-score 1.00
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · a predicted model of the same protein · chain D 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 1KXQ · PDBe 1KXQ · UniProt P00690
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