Research workbench
Crystal structure analysis of the radixin ferm domain complexed with adhesion molecule psgl-1
Analyse Crystal structure analysis of the radixin ferm domain complexed with adhesion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EMT
- Type
- protein
- Length
- 668 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Radixin; P-selectin glycoprotein ligand 1
- UniProt
- P26043, Q62170
- Pockets
- 15 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Radixin | protein | 313 | 35% helix, 23% strand | P26043 |
| C | P-selectin glycoprotein ligand 1 | protein | 16 | 0% helix, 25% strand | Q62170 |
| D | P-selectin glycoprotein ligand 1 | protein | 17 | 0% helix, 18% strand | Q62170 |
| E | P-selectin glycoprotein ligand 1 | protein | 9 | 0% helix, 44% strand | Q62170 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.60 | 0.77 | 30 | empty |
| 2 | 321 | 0.58 | 0.76 | 28 | empty |
| 3 | 379 | 0.56 | 0.74 | 41 | empty |
| 4 | 118 | 0.55 | 0.83 | 17 | empty |
| 5 | 354 | 0.55 | 0.74 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–D · 665 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 608 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 439 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 207 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2EMT · Crystal Structure Analysis of the radixin FERM domain complexed with adhesion molecule… · the same entry in another collection · chain E against E, TM-score 1.00
- P26043 · AlphaFold monomer V2.0 prediction for radixin (P26043) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q62170 · AlphaFold monomer V2.0 prediction for P-selectin glycoprotein ligand 1 (Q62170) · a predicted model of the same protein · chain E against A, TM-score 0.40
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 P26043
- Every structure of UniProt Q62170
- Elsewhere: RCSB PDB 2EMT · PDBe 2EMT · UniProt P26043 · UniProt Q62170
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.