Research workbench
Structure of a binary complex between homologous tetrameric legume lectins from butea monosperma and spatholobus parviflorus seeds
Analyse Structure of a binary complex between homologous tetrameric legume lectins from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M3C
- Type
- protein
- Length
- 1,952 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin alpha chain; Lectin beta chain; Seed lectin alpha chain; Seed lectin beta chain
- UniProt
- H2L2M6, H2L2M7, P86352, P86353
- Ligands
- ABU, CA, MN
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lectin alpha chain | protein | 249 | 8% helix, 43% strand | H2L2M6 |
| B, D | Lectin beta chain | protein | 239 | 5% helix, 45% strand | H2L2M7 |
| E, G | Seed lectin alpha chain | protein | 249 | 6% helix, 44% strand | P86352 |
| F, H | Seed lectin beta chain | protein | 239 | 4% helix, 45% strand | P86353 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · 6 copies · chains A, D, B, C, E, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 3 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.81 | 0.87 | 65 | empty |
| 2 | 415 | 0.80 | 0.89 | 48 | GOL |
| 3 | 537 | 0.80 | 0.87 | 63 | GOL |
| 4 | 560 | 0.78 | 0.84 | 72 | empty |
| 5 | 517 | 0.77 | 0.84 | 47 | empty |
Interfaces
13 interfaces between chains.
- B–C · 1070 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1043 Ų buried · 20 hydrogen bonds · protein-protein
- E–H · 1021 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1010 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 962 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4M3C · Structure of a binary complex between homologous tetrameric legume lectins from Butea… · the same entry in another collection · chain H against H, TM-score 1.00
- P86353 · AlphaFold monomer V2.0 prediction for seed lectin beta chain (P86353) · a predicted model of the same protein · chain F 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
- Every structure of UniProt H2L2M6
- Every structure of UniProt H2L2M7
- Every structure of UniProt P86352
- Every structure of UniProt P86353
- Elsewhere: RCSB PDB 4M3C · PDBe 4M3C · UniProt H2L2M6 · UniProt H2L2M7 · UniProt P86352 · UniProt P86353
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