Research workbench
Structure of the human TMED1 (P24GAMMA1) golgi dynamics domain
Analyse Structure of the human TMED1 (P24GAMMA1) golgi dynamics domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RRM
- Type
- protein
- Length
- 297 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane EMP24 domain-containing protein 1
- UniProt
- Q13445
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B | Transmembrane EMP24 domain-containing protein 1 | protein | 99 | 0% helix, 65% strand | Q13445 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.65 | 0.96 | 15 | MPD |
| 2 | 86 | 0.36 | 0.76 | 25 | empty |
| 3 | 52 | 0.30 | 0.76 | 15 | empty |
| 4 | 50 | 0.26 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–A · 804 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 348 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 314 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RRM · Structure of the human TMED1 (p24gamma1) Golgi dynamics Domain · the same entry in another collection · chain C against C, TM-score 1.00
- Q13445 · AlphaFold monomer V2.0 prediction for transmembrane EMP24 domain- containing protein 1… · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q13445
- Elsewhere: RCSB PDB 7RRM · PDBe 7RRM · UniProt Q13445
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