MolNFT v1 · #122274 · protein
Laminin A2LG45 I-form, G6/7 bound.
5IK8 · Laminin subunit alpha-2: “Laminin A2LG45 I-form, G6/7 bound.”. X-ray diffraction, 5 ligands (4MU, BDP, XYS), 5 pockets (best druggability 0.69). MolNFT v1 #122274 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IK8
- Type
- protein
- Length
- 759 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laminin subunit alpha-2
- UniProt
- Q60675
- Ligands
- 4MU, BDP, XYS, NAG, CA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laminin subunit alpha-2 | protein | 381 | 2% helix, 49% strand | Q60675 |
| B | Laminin subunit alpha-2 | protein | 378 | 2% helix, 50% strand | Q60675 |
Ligands and binding sites
- 4MU · 7-hydroxy-4-methyl-2H-chromen-2-one · ligand
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains B
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- FLC · Citrate anion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.69 | 0.77 | 72 | FLC |
| 2 | 129 | 0.53 | 0.81 | 19 | empty |
| 3 | 101 | 0.52 | 0.83 | 19 | EDO |
| 4 | 77 | 0.52 | 0.86 | 17 | empty |
| 5 | 176 | 0.44 | 0.74 | 25 | EDO |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5IK8 · Laminin A2LG45 I-form, G6/7 bound. · 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 Q60675
- Elsewhere: RCSB PDB 5IK8 · PDBe 5IK8 · UniProt Q60675
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