MolNFT v1 · #185981 · protein
Structure of codb, a cytosine transporter in an outward-facing conformation
7QOA · Cytosine permease: “Structure of codb, a cytosine transporter in an outward-facing conformation”. X-ray diffraction, 4 ligands (A6L, CYT, PEF), 12 pockets (best druggability 0.68). MolNFT v1 #185981 on GenesisL1: 3D structure…
- PDB
- 7QOA
- Type
- protein
- Length
- 801 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosine permease
- UniProt
- A0A857SHB2
- Ligands
- A6L, CYT, PEF, NA
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosine permease | protein | 401 | 80% helix, 0% strand | A0A857SHB2 |
| B | Cytosine permease | protein | 400 | 82% helix, 1% strand | A0A857SHB2 |
Ligands and binding sites
- A6L · 2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 5 copies · chains A, B
- CYT · 6-aminopyrimidin-2(1H)-one · ligand · 2 copies · chains A, B
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.68 | 0.75 | 57 | empty |
| 2 | 285 | 0.61 | 0.79 | 39 | CYT, A6L |
| 3 | 260 | 0.60 | 0.79 | 37 | CYT |
| 4 | 100 | 0.58 | 0.86 | 20 | A6L |
| 5 | 116 | 0.58 | 0.85 | 23 | A6L |
Interfaces
1 interface between chains.
- A–B · 816 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7QOA · Structure of CodB, a cytosine transporter in an outward-facing conformation · 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 A0A857SHB2
- Elsewhere: RCSB PDB 7QOA · PDBe 7QOA · UniProt A0A857SHB2
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