Research workbench
Crystal structure of P-selectin LECTIN/EGF domains
Analyse Crystal structure of P-selectin LECTIN/EGF domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G1Q
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P-selectin
- UniProt
- P16109
- Ligands
- CA
- Pockets
- 4 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | P-selectin | protein | 160 | 16% helix, 34% strand | P16109 |
| C | P-selectin | protein | 159 | 16% helix, 33% strand | P16109 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.39 | 0.76 | 21 | empty |
| 2 | 117 | 0.36 | 0.73 | 19 | empty |
| 3 | 101 | 0.35 | 0.73 | 14 | empty |
| 4 | 52 | 0.30 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 683 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
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 P16109
- Elsewhere: RCSB PDB 1G1Q · PDBe 1G1Q · UniProt P16109
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