MolNFT v1 · #120431 · protein
Crystal structure of amyp in complex with maltose
5H06: “Crystal structure of amyp in complex with maltose”. X-ray diffraction, 2 ligands (GLC, CA), 20 pockets (best druggability 0.77). MolNFT v1 #120431 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H06
- Type
- protein
- Length
- 1,990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyp
- Ligands
- GLC, CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Amyp | protein | 497 | 34% helix, 21% strand | — |
| B | Amyp | protein | 499 | 34% helix, 20% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.77 | 0.86 | 61 | GLC |
| 2 | 285 | 0.75 | 0.88 | 38 | empty |
| 3 | 244 | 0.73 | 0.88 | 31 | empty |
| 4 | 333 | 0.64 | 0.80 | 43 | empty |
| 5 | 123 | 0.59 | 0.85 | 26 | GLC |
Interfaces
6 interfaces between chains.
- A–B · 1130 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1117 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 289 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5H06 · Crystal structure of AmyP in complex with maltose · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 5H06 · PDBe 5H06
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