MolNFT v1 · #120048 · protein
The crystal structure of pecam-1 IGL1-2 trans-homophilic dimer
5GNI · Platelet endothelial cell adhesion molecule: “The crystal structure of pecam-1 IGL1-2 trans-homophilic dimer”. X-ray diffraction, 3 pockets (best druggability 0.41). MolNFT v1 #120048 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GNI
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet endothelial cell adhesion molecule
- UniProt
- P16284
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet endothelial cell adhesion molecule | protein | 196 | 2% helix, 59% strand | P16284 |
| B | Platelet endothelial cell adhesion molecule | protein | 198 | 2% helix, 61% strand | P16284 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.41 | 0.74 | 17 | empty |
| 2 | 96 | 0.38 | 0.76 | 18 | empty |
| 3 | 93 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1161 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GNI · The crystal structure of PECAM-1 IgL1-2 trans-homophilic dimer · the same entry in another collection · chain A against A, TM-score 1.00
- P16284 · AlphaFold monomer V2.0 prediction for platelet endothelial cell adhesion molecule (P16284) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P16284
- Elsewhere: RCSB PDB 5GNI · PDBe 5GNI · UniProt P16284
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