MolNFT v1 · #103306 · protein
Crystal structure of canavalia brasiliensis seed lectin (conbr) complexed with gamma-aminobutyric acid (GABA)
4PCR · Concanavalin-br: “Crystal structure of canavalia brasiliensis seed lectin (conbr) complexed with gamma-aminobutyric acid (GABA)”. X-ray diffraction, 3 ligands (ABU, CA, MN), 2 pockets (best druggability 0.41). MolNFT v1 #103306 on…
- PDB
- 4PCR
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-br
- UniProt
- P55915
- Ligands
- ABU, CA, MN
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Concanavalin-br | protein | 234 | 4% helix, 48% strand | P55915 |
| D | Concanavalin-br | protein | 232 | 4% helix, 45% strand | P55915 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 3 copies · chains A, D
- CA · Calcium ion · metal · 2 copies · chains A, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.41 | 0.80 | 15 | ABU |
| 2 | 51 | 0.35 | 0.79 | 13 | ABU |
Interfaces
1 interface between chains.
- A–D · 1003 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4PCR · Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- P55915 · AlphaFold monomer V2.0 prediction for concanavalin-br (P55915) · a predicted model of the same protein · chain D 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 P55915
- Elsewhere: RCSB PDB 4PCR · PDBe 4PCR · UniProt P55915
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