MolNFT v1 · #120430 · protein
Crystal structure of amyp E221Q in complex with maltotriose
5H05: “Crystal structure of amyp E221Q in complex with maltotriose”. X-ray diffraction, 2 ligands (GLC, CA), 20 pockets (best druggability 0.73). MolNFT v1 #120430 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H05
- Type
- protein
- Length
- 1,983 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyp
- Ligands
- GLC, CA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Amyp | protein | 497 | 33% helix, 21% strand | — |
| B | Amyp | protein | 494 | 33% helix, 20% strand | — |
| C | Amyp | protein | 495 | 34% helix, 20% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 12 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.73 | 0.87 | 30 | empty |
| 2 | 271 | 0.73 | 0.86 | 33 | empty |
| 3 | 209 | 0.70 | 0.87 | 38 | GLC |
| 4 | 119 | 0.60 | 0.86 | 23 | GLC |
| 5 | 109 | 0.58 | 0.86 | 22 | GLC |
Interfaces
6 interfaces between chains.
- C–D · 1159 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1125 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 279 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 251 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5H05 · Crystal structure of AmyP E221Q in complex with MALTOTRIOSE · 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
- Elsewhere: RCSB PDB 5H05 · PDBe 5H05
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