Research workbench
Structure of the exo-alpha-L-galactosidase BPGH29 (D264N mutant) from bacteroides plebeius in complex with paranitrophenyl-alpha-L- galactopyranoside
Analyse Structure of the exo-alpha-L-galactosidase BPGH29 (D264N mutant) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LNP
- Type
- protein
- Length
- 2,221 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-alpha-L-galactosidase
- UniProt
- B5CYA5
- Ligands
- Y9Y, NA, NI, CA, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Exo-alpha-L-galactosidase | protein | 565 | 27% helix, 26% strand | B5CYA5 |
| D | Exo-alpha-L-galactosidase | protein | 543 | 27% helix, 29% strand | B5CYA5 |
| E | Exo-alpha-L-galactosidase | protein | 548 | 27% helix, 27% strand | B5CYA5 |
Ligands and binding sites
- Y9Y · paranitrophenyl-alpha-L-galactopyranoside · ligand · 4 copies · chains A, C, D, E
- NA · Sodium ion · metal · 10 copies · chains A, C, D, E
- NI · Nickel (II) ion · metal · 9 copies · chains A, C, D, E
- CA · Calcium ion · metal · 4 copies · chains A, C, D, E
- CL · Chloride ion · ion · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.77 | 0.79 | 103 | empty |
| 2 | 379 | 0.58 | 0.75 | 42 | NA |
| 3 | 215 | 0.57 | 0.80 | 29 | empty |
| 4 | 407 | 0.55 | 0.73 | 42 | NI |
| 5 | 176 | 0.53 | 0.79 | 35 | empty |
Interfaces
4 interfaces between chains.
- C–D · 662 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 239 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LNP · Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides… · 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 B5CYA5
- Elsewhere: RCSB PDB 7LNP · PDBe 7LNP · UniProt B5CYA5
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