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
- 5T5O
- Type
- protein
- Length
- 2,340 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin; Tn-peptide ACE-gly-val-thr-ser-ala
- UniProt
- P86993
- Ligands
- ACE, A2G, CA
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Lectin | protein | 229 | 7% helix, 48% strand | P86993 |
| a, b, c, d, e, f, g, h, i, j | Tn-peptide ACE-gly-val-thr-ser-ala | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 10 copies · chains A, a, B, b, F, C, c, I, d, e, f, g, J, h, i, G, j
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 10 copies · chains A, a, B, b, F, C, c, I, D, d, E, e, f, G, g, J, H, h, i, j
- CA · Calcium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.65 | 0.94 | 21 | A2G |
| 2 | 71 | 0.64 | 0.92 | 22 | A2G |
| 3 | 415 | 0.63 | 0.78 | 53 | empty |
| 4 | 69 | 0.63 | 0.92 | 22 | A2G |
| 5 | 63 | 0.62 | 0.92 | 23 | A2G |
Interfaces
27 interfaces between chains.
- G–H · 896 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 892 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 890 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 870 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 862 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent, 10 glycan (covalent ligand, O-glycosylation).
Compared structures
- 5T5O · Lectin from bauhinia forficata in complex with tn-peptide · the same entry in another collection · chain j against j, 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 P86993
- Elsewhere: RCSB PDB 5T5O · PDBe 5T5O · UniProt P86993
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