MolNFT v1 · #134812 · protein
Crystal structure of dioclea reflexa seed lectin (drfl) in complex with X-man
5TG3 · Dioclea reflexa lectin: “Crystal structure of dioclea reflexa seed lectin (drfl) in complex with X-man”. X-ray diffraction, 3 ligands (XMM, CA, MN), 3 pockets (best druggability 0.83). MolNFT v1 #134812 on GenesisL1: 3D structure…
- PDB
- 5TG3
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioclea reflexa lectin
- Ligands
- XMM, CA, MN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dioclea reflexa lectin | protein | 230 | 4% helix, 45% strand | — |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.83 | 0.84 | 143 | empty |
| 2 | 50 | 0.68 | 0.96 | 20 | empty |
| 3 | 116 | 0.62 | 0.87 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 984 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 980 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 739 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 728 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5TG3 · Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5TG3 · PDBe 5TG3
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