MolNFT v1 · #12989 · protein
Camelid vhh domains in complex with porcine pancreatic alpha-amylase
1KXT · Alpha-amylase, pancreatic: “Camelid vhh domains in complex with porcine pancreatic alpha-amylase”. X-ray diffraction, 2 ligands (CA, CL), 19 pockets (best druggability 0.67). MolNFT v1 #12989 on GenesisL1: 3D structure, binding…
- PDB
- 1KXT
- Type
- protein
- Length
- 1,857 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amylase, pancreatic; Immunoglobulin vhh fragment
- EC
- 3.2.1.1
- UniProt
- P00690
- Ligands
- CA, CL
- Pockets
- 19 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Alpha-amylase, pancreatic (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P00690 |
| B, D, F | Immunoglobulin vhh fragment | protein | 123 | 2% helix, 52% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C, E
- CL · Chloride ion · ion · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.67 | 0.80 | 53 | empty |
| 2 | 403 | 0.65 | 0.79 | 55 | empty |
| 3 | 371 | 0.60 | 0.77 | 36 | empty |
| 4 | 131 | 0.46 | 0.78 | 29 | empty |
| 5 | 196 | 0.45 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 868 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 862 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 854 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 131 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 1KXT · Camelid VHH Domains in Complex with Porcine Pancreatic alpha-Amylase · the same entry in another collection · chain F against F, TM-score 1.00
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · a predicted model of the same protein · chain C 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 1KXT · PDBe 1KXT · UniProt P00690
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