MolNFT v1 · #71461 · protein
X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)
3MEZ · Mannose-specific lectin 3 chain 1: “X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus)”. X-ray diffraction, 5 pockets (best druggability 0.47). MolNFT v1 #71461 on GenesisL1: 3D structure…
- PDB
- 3MEZ
- Type
- protein
- Length
- 446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-specific lectin 3 chain 1; Mannose-specific lectin 3 chain 2
- UniProt
- P86626
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannose-specific lectin 3 chain 1 | protein | 111 | 0% helix, 39% strand | P86626 |
| B | Mannose-specific lectin 3 chain 2 | protein | 113 | 0% helix, 43% strand | P86626 |
| C | Mannose-specific lectin 3 chain 1 | protein | 110 | 0% helix, 39% strand | P86626 |
| D | Mannose-specific lectin 3 chain 2 | protein | 112 | 0% helix, 44% strand | P86626 |
Ligands and binding sites
- FMT · Formic acid · additive · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.47 | 0.77 | 26 | GOL |
| 2 | 126 | 0.45 | 0.77 | 27 | GOL, FMT |
| 3 | 61 | 0.44 | 0.83 | 19 | empty |
| 4 | 83 | 0.42 | 0.79 | 17 | FMT |
| 5 | 81 | 0.39 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1520 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1504 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1119 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3MEZ · X-ray structural analysis of a mannose specific lectin from dutch crocus (crocus vernus) · the same entry in another collection · chain D against D, TM-score 1.00
- P86626 · AlphaFold monomer V2.0 prediction for mannose-specific lectin 3 (P86626) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P86626
- Elsewhere: RCSB PDB 3MEZ · PDBe 3MEZ · UniProt P86626
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