Research workbench
Crystal structure of PDGH110B D344N in complex with alpha-(1,3)- galactobiose
Analyse Crystal structure of PDGH110B D344N in complex with alpha-(1,3)- galactobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JWF
- Type
- protein
- Length
- 2,330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 110
- Ligands
- MLT, GAL, GLA, CA, IOD, CL
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 110 | protein | 584 | 7% helix, 46% strand | — |
| B, C, D | Glycoside hydrolase family 110 | protein | 582 | 7% helix, 46% strand | — |
Ligands and binding sites
- MLT · D-malate · ligand · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 119 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 50 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D
- MLA · Malonic acid · additive · chains D
- MLI · Malonate ion · additive · chains D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.85 | 0.87 | 87 | GAL, GLA, IOD |
| 2 | 150 | 0.66 | 0.88 | 32 | GAL, GLA, EDO, IOD |
| 3 | 172 | 0.54 | 0.80 | 35 | GAL, GLA, IOD |
| 4 | 228 | 0.53 | 0.77 | 35 | IOD |
| 5 | 250 | 0.53 | 0.76 | 32 | IOD |
Interfaces
4 interfaces between chains.
- A–B · 2380 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 506 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 241 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7JWF · Crystal structure of PdGH110B D344N in complex with alpha-(1,3)-galactobiose · 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 7JWF · PDBe 7JWF
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