MolNFT v1 · #41129 · protein
Crystal structure of recombinant dioclea grandiflora lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose
2JE9 · Lectin alpha chain: “Crystal structure of recombinant dioclea grandiflora lectin complexed with…”. X-ray diffraction, 4 ligands (XMM, CA, MN), 7 pockets (best druggability 0.87). MolNFT v1 #41129 on GenesisL1: 3D structure, binding…
- PDB
- 2JE9
- Type
- protein
- Length
- 952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin alpha chain
- UniProt
- P08902
- Ligands
- XMM, CA, MN, SO4
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lectin alpha chain | protein | 238 | 4% helix, 47% strand | P08902 |
Ligands and binding sites
- XMM · 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.87 | 0.88 | 133 | empty |
| 2 | 82 | 0.62 | 0.90 | 27 | empty |
| 3 | 72 | 0.54 | 0.86 | 27 | empty |
| 4 | 113 | 0.48 | 0.79 | 23 | SO4 |
| 5 | 68 | 0.47 | 0.83 | 21 | SO4 |
Interfaces
5 interfaces between chains.
- A–D · 1145 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1134 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1120 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1097 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2JE9 · Crystal structure of recombinant dioclea grandiflora lectin complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P08902 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P08902) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P08902
- Elsewhere: RCSB PDB 2JE9 · PDBe 2JE9 · UniProt P08902
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