MolNFT v1 · #127240 · protein
Sialidase BT_1020
5MQR · Beta-L-arabinobiosidase: “Sialidase BT_1020”. X-ray diffraction, 2 ligands (CA, NA), 10 pockets (best druggability 0.65). MolNFT v1 #127240 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MQR
- Type
- protein
- Length
- 1,082 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-L-arabinobiosidase
- EC
- 3.2.1.187
- UniProt
- A0A0P0FQG4
- Ligands
- CA, NA
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-L-arabinobiosidase (EC 3.2.1.187) | protein | 1082 | 22% helix, 27% strand | A0A0P0FQG4 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.65 | 0.82 | 50 | CA |
| 2 | 207 | 0.64 | 0.83 | 23 | empty |
| 3 | 318 | 0.57 | 0.76 | 44 | NA |
| 4 | 140 | 0.53 | 0.80 | 25 | EPE |
| 5 | 160 | 0.47 | 0.76 | 30 | empty |
Modifications
Observed in the structure: 36 modified (engineered, phosphorylation).
Compared structures
- 5MQR · Sialidase BT_1020 · 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
- Every structure of UniProt A0A0P0FQG4
- Elsewhere: RCSB PDB 5MQR · PDBe 5MQR · UniProt A0A0P0FQG4
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