MolNFT v1 · #114511 · protein
Crystal structure of bacillus licheniformis trehalose-6-phosphate hydrolase (trea), mutant R201Q, in complex with png
5BRP · Glycoside hydrolase family 13: “Crystal structure of bacillus licheniformis trehalose-6-phosphate hydrolase (trea), mutant R201Q, in complex…”. X-ray diffraction, 2 ligands (PNG, MG), 20 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5BRP
- Type
- protein
- Length
- 2,220 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 13
- EC
- 3.2.1.93
- UniProt
- Q65MI2
- Ligands
- PNG, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycoside hydrolase family 13 (EC 3.2.1.93) | protein | 555 | 35% helix, 18% strand | Q65MI2 |
Ligands and binding sites
- PNG · 4-nitrophenyl alpha-D-glucopyranoside · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.80 | 0.83 | 56 | empty |
| 2 | 620 | 0.76 | 0.82 | 50 | PNG |
| 3 | 548 | 0.76 | 0.83 | 44 | PNG |
| 4 | 601 | 0.76 | 0.82 | 49 | PNG |
| 5 | 708 | 0.73 | 0.79 | 59 | empty |
Interfaces
5 interfaces between chains.
- A–D · 761 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 683 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 475 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
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 Q65MI2
- Elsewhere: RCSB PDB 5BRP · PDBe 5BRP · UniProt Q65MI2
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