MolNFT v1 · #120014 · protein
Crystal structure of GRASP55 grasp domain in complex with jam-C C- terminus
5GMI · Golgi reassembly-stacking protein 2: “Crystal structure of GRASP55 grasp domain in complex with jam-C C- terminus”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #120014 on GenesisL1: 3D structure, binding sites…
- PDB
- 5GMI
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Golgi reassembly-stacking protein 2; Junctional adhesion molecule C
- UniProt
- Q99JX3, Q9D8B7
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Golgi reassembly-stacking protein 2 | protein | 223 | 11% helix, 30% strand | Q99JX3 |
| C, D | Junctional adhesion molecule C | protein | 5 | 0% helix, 40% strand | Q9D8B7 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.65 | 0.83 | 41 | empty |
| 2 | 171 | 0.62 | 0.84 | 30 | empty |
| 3 | 166 | 0.60 | 0.83 | 30 | empty |
| 4 | 358 | 0.56 | 0.75 | 35 | empty |
| 5 | 52 | 0.50 | 0.87 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1264 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 484 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5GMI · Crystal Structure of GRASP55 GRASP domain in complex with JAM-C C-terminus · the same entry in another collection · chain A against A, 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 0.88
- Q9D8B7 · AlphaFold monomer V2.0 prediction for junctional adhesion molecule C (Q9D8B7) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 Q9D8B7
- Elsewhere: RCSB PDB 5GMI · PDBe 5GMI · UniProt Q99JX3 · UniProt Q9D8B7
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