Research workbench
Soybean agglutinin from glycine max in complex with the antigen tn
Analyse Soybean agglutinin from glycine max in complex with the antigen tn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D69
- Type
- protein
- Length
- 2,822 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin; Short antigen peptide
- UniProt
- P05046
- Ligands
- NAG, A2G, MN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 11 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, I | Lectin | protein | 234 | 3% helix, 47% strand | P05046 |
| B | Lectin | protein | 232 | 4% helix, 47% strand | P05046 |
| C, E | Lectin | protein | 231 | 4% helix, 47% strand | P05046 |
| G | Lectin | protein | 233 | 4% helix, 46% strand | P05046 |
| H, K, L | Lectin | protein | 232 | 4% helix, 47% strand | P05046 |
| J | Lectin | protein | 232 | 4% helix, 47% strand | P05046 |
| O, X | Short antigen peptide | protein | 4 | 0% helix, 0% strand | — |
| P, Q, T, W, Z | Short antigen peptide | protein | 2 | 0% helix, 0% strand | — |
| R, V, Y | Short antigen peptide | protein | 3 | 0% helix, 0% strand | — |
| S | Short antigen peptide | protein | 1 | 0% helix, 0% strand | — |
| U | Short antigen peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, E, B, C, D, F, G, H, I, K, J, L
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 12 copies · chains A, P, B, R, C, S, D, T, E, U, F, X, G, W, H, Z, I, O, J, Q, K, Y, L, V
- MN · Manganese (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 960 | 0.85 | 0.86 | 105 | empty |
| 2 | 1081 | 0.80 | 0.81 | 114 | empty |
| 3 | 487 | 0.75 | 0.83 | 56 | A2G |
| 4 | 515 | 0.70 | 0.79 | 47 | empty |
| 5 | 489 | 0.69 | 0.80 | 44 | empty |
Interfaces
39 interfaces between chains.
- H–J · 844 Ų buried · 16 hydrogen bonds · protein-protein
- D–L · 829 Ų buried · 18 hydrogen bonds · protein-protein
- B–K · 821 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 719 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 719 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan (N-glycosylation, O-glycosylation).
Compared structures
- 4D69 · SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn · the same entry in another collection · chain Y against Y, 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 P05046
- Elsewhere: RCSB PDB 4D69 · PDBe 4D69 · UniProt P05046
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