Research workbench
Lectin from bauhinia forficata in complex with tn-peptide
Analyse Lectin from bauhinia forficata in complex with tn-peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T5L
- Type
- protein
- Length
- 465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin; Tn antigen ACE-ser-ser-val-gly
- UniProt
- P86993
- Ligands
- ACE, A2G, CA, CL
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 229 | 6% helix, 49% strand | P86993 |
| a | Tn antigen ACE-ser-ser-val-gly | protein | 3 | 0% helix, 0% strand | — |
| b | Tn antigen ACE-ser-ser-val-gly | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, a, B, b
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, a, B, b
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.47 | 0.81 | 19 | A2G |
| 2 | 107 | 0.45 | 0.79 | 22 | EDO |
| 3 | 89 | 0.45 | 0.80 | 20 | A2G |
| 4 | 99 | 0.44 | 0.79 | 19 | EDO |
| 5 | 172 | 0.39 | 0.72 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 852 Ų buried · 17 hydrogen bonds · protein-protein
- A–a · 131 Ų buried · 2 hydrogen bonds · protein-protein
- B–b · 117 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 glycan (covalent ligand, O-glycosylation).
Compared structures
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 P86993
- Elsewhere: RCSB PDB 5T5L · PDBe 5T5L · UniProt P86993
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