Research workbench
Pmtcd peptide exporter basket domain
Analyse Pmtcd peptide exporter basket domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U2D
- Type
- protein
- Length
- 257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter ATP-binding protein
- UniProt
- X5EJW5
- Ligands
- IOD, SO4
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter ATP-binding protein | protein | 66 | 35% helix, 26% strand | X5EJW5 |
| B, D | ABC transporter ATP-binding protein | protein | 64 | 41% helix, 30% strand | X5EJW5 |
| C | ABC transporter ATP-binding protein | protein | 63 | 37% helix, 30% strand | X5EJW5 |
Ligands and binding sites
- IOD · Iodide ion · ion · 7 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.57 | 0.78 | 28 | empty |
| 2 | 50 | 0.30 | 0.76 | 15 | IOD |
Interfaces
4 interfaces between chains.
- A–B · 714 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 280 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6U2D · PmtCD peptide exporter basket domain · the same entry in another collection · chain A against A, TM-score 1.00
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 X5EJW5
- Elsewhere: RCSB PDB 6U2D · PDBe 6U2D · UniProt X5EJW5
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