MolNFT v1 · #170713 · protein
Ecla N-terminal domain; plla-like lectin
6YGQ · Pa-I galactophilic lectin: “Ecla N-terminal domain; plla-like lectin”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.60). MolNFT v1 #170713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YGQ
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin
- UniProt
- A0A5E3W395
- Ligands
- CA
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pa-I galactophilic lectin | protein | 121 | 0% helix, 51% strand | A0A5E3W395 |
| B, C | Pa-I galactophilic lectin | protein | 120 | 0% helix, 51% strand | A0A5E3W395 |
| D | Pa-I galactophilic lectin | protein | 119 | 0% helix, 51% strand | A0A5E3W395 |
Ligands and binding sites
- CA · Calcium 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.60 | 0.75 | 43 | empty |
| 2 | 171 | 0.60 | 0.83 | 29 | empty |
| 3 | 287 | 0.55 | 0.76 | 38 | empty |
| 4 | 100 | 0.44 | 0.79 | 22 | empty |
| 5 | 123 | 0.40 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1338 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1254 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 671 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6YGQ · EclA N-terminal domain; PllA-like lectin · 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
- Every structure of UniProt A0A5E3W395
- Elsewhere: RCSB PDB 6YGQ · PDBe 6YGQ · UniProt A0A5E3W395
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.