Research workbench
Crystal structure of GRASP55 grasp domain in complex with jam-B C- terminus
Analyse Crystal structure of GRASP55 grasp domain in complex with jam-B C- terminus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GMJ
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Golgi reassembly-stacking protein 2; Junctional adhesion molecule B
- UniProt
- Q99JX3, Q9JI59
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Golgi reassembly-stacking protein 2 | protein | 223 | 11% helix, 30% strand | Q99JX3 |
| B | Golgi reassembly-stacking protein 2 | protein | 224 | 13% helix, 30% strand | Q99JX3 |
| C | Junctional adhesion molecule B | protein | 8 | 0% helix, 25% strand | Q9JI59 |
| D | Junctional adhesion molecule B | protein | 6 | 0% helix, 33% strand | Q9JI59 |
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 | 329 | 0.69 | 0.83 | 52 | empty |
| 2 | 261 | 0.62 | 0.80 | 29 | empty |
| 3 | 177 | 0.55 | 0.80 | 26 | empty |
| 4 | 336 | 0.54 | 0.75 | 34 | empty |
| 5 | 62 | 0.47 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1271 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 688 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5GMJ · Crystal Structure of GRASP55 GRASP domain in complex with JAM-B C-terminus · the same entry in another collection · chain D against D, TM-score 1.00
- Q99JX3 · AlphaFold monomer V2.0 prediction for golgi reassembly-stacking protein 2 (Q99JX3) · a predicted model of the same protein · chain A against A, TM-score 0.87
- Q9JI59 · AlphaFold monomer V2.0 prediction for junctional adhesion molecule B (Q9JI59) · a predicted model of the same protein · chain D against A, TM-score 0.58
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 Q99JX3
- Every structure of UniProt Q9JI59
- Elsewhere: RCSB PDB 5GMJ · PDBe 5GMJ · UniProt Q99JX3 · UniProt Q9JI59
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