Research workbench
PEPT - CIM
Analyse PEPT - CIM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6K
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Di-or TRIPEPTIDE:H+ symporter
- UniProt
- Q5M4H8
- Ligands
- 97M, 97N, PO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Di-or TRIPEPTIDE:H+ symporter | protein | 448 | 82% helix, 1% strand | Q5M4H8 |
Ligands and binding sites
- 97M · (2R)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate · ligand · 8 copies · chains A
- 97N · (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate · ligand · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.82 | 0.86 | 46 | empty |
| 2 | 539 | 0.66 | 0.76 | 63 | empty |
| 3 | 50 | 0.37 | 0.80 | 13 | empty |
| 4 | 58 | 0.29 | 0.74 | 14 | empty |
| 5 | 57 | 0.29 | 0.75 | 20 | empty |
Compared structures
- 5D6K · PepT - CIM · 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 Q5M4H8
- Elsewhere: RCSB PDB 5D6K · PDBe 5D6K · UniProt Q5M4H8
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