MolNFT v1 · #169430 · protein
X-ray crystal structure of the mouse cmp-sialic acid transporter in complex with 5-methyl cmp
6XBO: “X-ray crystal structure of the mouse cmp-sialic acid transporter in complex with 5-methyl cmp”. X-ray diffraction, 1 ligand (5MC), 4 pockets (best druggability 0.82). MolNFT v1 #169430 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XBO
- Type
- protein
- Length
- 319 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmp-sialic acid transporter
- UniProt
- Q61420
- Ligands
- 5MC
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cmp-sialic acid transporter | protein | 319 | 80% helix, 0% strand | Q61420 |
Ligands and binding sites
- 5MC · 5-methylcytidine-5'-monophosphate · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 13 copies · chains A
- 2PE · Nonaethylene glycol · additive · 2 copies · chains A
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 | 707 | 0.82 | 0.86 | 87 | 5MC |
| 2 | 90 | 0.33 | 0.73 | 19 | OLC |
| 3 | 67 | 0.28 | 0.73 | 13 | empty |
| 4 | 56 | 0.28 | 0.73 | 15 | empty |
Compared structures
- 6XBO · X-ray crystal structure of the mouse CMP-Sialic acid transporter in complex with 5-methyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q61420 · AlphaFold monomer V2.0 prediction for cmp-sialic acid transporter (Q61420) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q61420
- Elsewhere: RCSB PDB 6XBO · PDBe 6XBO · UniProt Q61420
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