MolNFT v1 · #34055 · protein
Cratylia floribunda seed lectin crystallized at basic pH
2D3P · Lectin alpha chain: “Cratylia floribunda seed lectin crystallized at basic pH”. X-ray diffraction, 2 ligands (CA, MN), 4 pockets (best druggability 0.87). MolNFT v1 #34055 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2D3P
- Type
- protein
- Length
- 944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin alpha chain
- UniProt
- P81517
- Ligands
- CA, MN
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lectin alpha chain | protein | 236 | 4% helix, 46% strand | P81517 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.87 | 0.88 | 108 | empty |
| 2 | 72 | 0.50 | 0.84 | 24 | empty |
| 3 | 163 | 0.39 | 0.72 | 27 | empty |
| 4 | 151 | 0.39 | 0.73 | 32 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1185 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1154 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1142 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1141 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P81517
- Elsewhere: RCSB PDB 2D3P · PDBe 2D3P · UniProt P81517
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