Research workbench
Lecb (pa-lii) in complex with core trimannoside
Analyse Lecb (pa-lii) in complex with core trimannoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OVS
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein lecb
- Ligands
- MAN, CA
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 71% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical protein lecb | protein | 114 | 0% helix, 71% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.35 | 0.74 | 19 | empty |
| 2 | 83 | 0.30 | 0.72 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1319 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1277 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 521 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 520 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 224 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1OVS · LecB (PA-LII) in complex with core trimannoside · 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 1OVS · PDBe 1OVS
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