Research workbench
Crystal structure of SPGH92 in complex with mannose
Analyse Crystal structure of SPGH92 in complex with mannose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SWI
- Type
- protein
- Length
- 2,746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar hydrolase
- UniProt
- A0A0Y0HIE3
- Ligands
- BMA, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sugar hydrolase | protein | 693 | 31% helix, 27% strand | A0A0Y0HIE3 |
| A | Sugar hydrolase | protein | 692 | 32% helix, 26% strand | A0A0Y0HIE3 |
| C | Sugar hydrolase | protein | 680 | 32% helix, 26% strand | A0A0Y0HIE3 |
| D | Sugar hydrolase | protein | 681 | 32% helix, 27% strand | A0A0Y0HIE3 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A, C, D
- CA · Calcium ion · metal · 4 copies · chains B, A, C, D
- GOL · Glycerol · additive · 16 copies · chains B, A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.81 | 0.82 | 120 | empty |
| 2 | 768 | 0.80 | 0.84 | 107 | GOL |
| 3 | 339 | 0.75 | 0.86 | 45 | GOL, BMA |
| 4 | 522 | 0.75 | 0.83 | 56 | GOL, BMA, CA |
| 5 | 513 | 0.74 | 0.82 | 55 | CA, GOL, BMA |
Interfaces
6 interfaces between chains.
- A–C · 1407 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1349 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1067 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1058 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5SWI · Crystal structure of SpGH92 in complex with mannose · the same entry in another collection · chain B against B, 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 A0A0Y0HIE3
- Elsewhere: RCSB PDB 5SWI · PDBe 5SWI · UniProt A0A0Y0HIE3
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