Research workbench
Crystal structure of recombinant dioclea grandiflora lectin mutant E123A-H131N-K132Q complexed with 5-bromo-4-chloro-3-indolyl-a-D- mannose
Analyse Crystal structure of recombinant dioclea grandiflora lectin mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JEC
- 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, MN, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lectin alpha chain | protein | 238 | 4% helix, 45% 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
- MN · Manganese (II) ion · metal · 8 copies · chains A, D, B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.79 | 0.89 | 71 | MN |
| 2 | 245 | 0.76 | 0.90 | 56 | MN |
| 3 | 69 | 0.74 | 0.98 | 27 | empty |
| 4 | 71 | 0.71 | 0.96 | 27 | empty |
| 5 | 90 | 0.68 | 0.93 | 23 | MN |
Interfaces
6 interfaces between chains.
- C–D · 1195 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1110 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1065 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 927 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2JEC · crystal structure of recombinant DiocleA grandiflora lectin mutant E123A-H131N-K132Q… · 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 2JEC · PDBe 2JEC · UniProt P08902
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