Difference between revisions of "AtomSets/Carbohydrate"
AngelHerraez (talk | contribs) (Monosaccharides: SOL and SOE added) |
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= 'carbohydrate' atom set = | = 'carbohydrate' atom set = | ||
| − | ''(Updated to Jmol | + | ''(Updated to Jmol 16.1.9)'' |
Atoms are included in this set according to the name of the residue (group) they belong to: | Atoms are included in this set according to the name of the residue (group) they belong to: | ||
| Line 13: | Line 13: | ||
[AHR] = alpha-L-arabinofuranose | [AHR] = alpha-L-arabinofuranose | ||
| + | |||
| + | [ALL] = beta-D-allopyranose | ||
[AMU] = N-acetyl-beta-muramic acid | [AMU] = N-acetyl-beta-muramic acid | ||
| Line 57: | Line 59: | ||
[GUP] = alpha-L-gulopyranose | [GUP] = alpha-L-gulopyranose | ||
| + | |||
| + | [GXL] = alpha-L-galactopyranose | ||
[LAT] = beta-lactose | [LAT] = beta-lactose | ||
| Line 97: | Line 101: | ||
[SLB] = 5-N-acetyl-beta-D-neuraminic acid (see also SIA) | [SLB] = 5-N-acetyl-beta-D-neuraminic acid (see also SIA) | ||
| + | |||
| + | [SOE] = α-L-sorbopyranose | ||
| + | |||
| + | [SOL] = L-sorbose | ||
[SOR] = D-glucitol = D-sorbitol | [SOR] = D-glucitol = D-sorbitol | ||
| Line 135: | Line 143: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <th rowspan=" | + | <th rowspan="3">galactose</th> |
| − | <td rowspan=" | + | <td rowspan="3">pyranose</td> |
<td>α-D-Gal<sub>p</sub></td> | <td>α-D-Gal<sub>p</sub></td> | ||
<td>[GLA]</td> | <td>[GLA]</td> | ||
| Line 143: | Line 151: | ||
<td>β-D-Gal<sub>p</sub></td> | <td>β-D-Gal<sub>p</sub></td> | ||
<td>[GAL]</td> | <td>[GAL]</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>α-L-Gal<sub>p</sub></td> | ||
| + | <td>[GXL]</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 238: | Line 250: | ||
<td>α-L-sorbopyranose</td> | <td>α-L-sorbopyranose</td> | ||
<td>[SOE]</td> | <td>[SOE]</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <th>allose</th> | ||
| + | <td>pyranose</td> | ||
| + | <td>β-D-allopyranose</td> | ||
| + | <td>[ALL]</td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
| Line 297: | Line 315: | ||
== References == | == References == | ||
| − | * RCSB PDB [http://ligand-expo.rcsb.org/ld-search.html `Ligand | + | * RCSB PDB [http://ligand-expo.rcsb.org/ld-search.html `Ligand Expo´ Chemical Component Search Tools] |
| + | * [PDBe ligand dictionary https://www.ebi.ac.uk/pdbe-srv/pdbechem/] | ||
Revision as of 14:38, 24 April 2023
Contents
'carbohydrate' atom set
(Updated to Jmol 16.1.9)
Atoms are included in this set according to the name of the residue (group) they belong to:
Alphabetic
[A2G] = N-acetyl-alpha-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-alpha-D-galactopyranose (see also NGA)
[AFL] = <fucose> obsolete, replaced with FUL
[AGC] = <glucose> obsolete, replaced with GLC
[AHR] = alpha-L-arabinofuranose
[ALL] = beta-D-allopyranose
[AMU] = N-acetyl-beta-muramic acid
[ARA] = alpha-L-arabinopyranose
[ARB] = beta-L-arabinopyranose
[BDF] = beta-D-fructopyranose (see also FRU)
[BDR] = beta-D-ribofuranose
[BGC] = beta-D-glucopyranose (see also GLC)
[BMA] = beta-D-mannopyranose (see also MAN)
[CBI] = cellobiose
[CT3] = beta-cellotriose
[CTR] = cellotriose
[CTT] = cellotetraose
[FCA] = alpha-D-fucose (see also FCB, FUC, FUL)
[FCB] = beta-D-fucose (see also FCA, FUC, FUL)
[FRU] = beta-D-fructofuranose (see also BDF)
[FUC] = alpha-L-fucose (see also FCA, FCB, FUL)
[FUL] = beta-L-fucose (see also FCA, FCB, FUC)
[GAL] = beta-D-galactopyranose (see also GLA)
[GCU] = alpha-D-glucopyranuronic acid (glucuronic acid)
[GLA] = alpha-D-galactopyranose (see also GAL)
[GLB] = <galactose> obsolete, replaced with GAL
[GLC] = alpha-D-glucopyranose (see also BGC)
[GUP] = alpha-L-gulopyranose
[GXL] = alpha-L-galactopyranose
[LAT] = beta-lactose
[LBT] = alpha-lactose
[LXC] = beta-L-xylopyranose
[MAB] = mannobiose
[MAL] = maltose
[MAN] = alpha-D-mannopyranose (see also BMA)
[MLR] = maltotriose
[MTL] = D-mannitol
[MTT] = maltotetraose
[NAG] = N-acetyl-beta-D-glucosamine = β-GlcNAc = 2-(acetylamino)-2-deoxy-beta-D-glucopyranose) (see also NDG)
[NAN] = <sialic> obsolete, replaced with SIA
[NDG] = N-acetyl-alpha-D-glucosamine = α-GlcNAc = 2-(acetylamino)-2-deoxy-alpha-D-glucopyranose) (see also NAG)
[NGA] = N-acetyl-beta-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-beta-D-galactopyranose (see also A2G)
[RAA] = <rhamnose> obsolete, replaced with RAM
[RAM] = alpha-L-rhamnose
[RHA] = 6-deoxy-mannose-1'-phosphate
[RIB] = alpha-D-ribofuranose
[RIP] = beta-D-ribopyranose
[SIA] = 5-N-acetyl-alpha-D-neuraminic acid (see also SLB)
[SLB] = 5-N-acetyl-beta-D-neuraminic acid (see also SIA)
[SOE] = α-L-sorbopyranose
[SOL] = L-sorbose
[SOR] = D-glucitol = D-sorbitol
[SUC] = sucrose
[TRE] = trehalose
[XYL] = D-xylitol
[XYP] = beta-D-xylopyranose
[XYS] = alpha-D-xylopyranose
Cathegorized
Monosaccharides
| glucose | pyranose | α-D-Glcp | [GLC] |
|---|---|---|---|
| β-D-Glcp | [BGC] | ||
| fructose | furanose | β-D-Fruf | [FRU] |
| pyranose | β-D-Frup | [BDF] | |
| galactose | pyranose | α-D-Galp | [GLA] |
| β-D-Galp | [GAL] | ||
| α-L-Galp | [GXL] | ||
| mannose | pyranose | α-D-Manp | [MAN] |
| β-D-Manp | [BMA] | ||
| ribose | furanose | α-D-Ribf | [RIB] |
| β-D-Ribf | [BDR] | ||
| pyranose | β-D-Ribp | [RIP] | |
| fucose | pyranose | α-D-Fucp | [FCA] |
| β-D-Fucp | [FCB] | ||
| α-L-Fucp | [FUC] | ||
| β-L-Fucp | [FUL] | ||
| xylose | pyranose | α-D-Xylp | [XYS] |
| β-D-Xylp | [XYP] | ||
| β-L-Xylp | [LXC] | ||
| arabinose | furanose | α-L-Araf | [AHR] |
| pyranose | α-L-Arap | [ARA] | |
| β-L-Arap | [ARB] | ||
| gulose | pyranose | α-L-Gulp | [GUP] |
| rhamnose | pyranose | α-L-Rhap | [RAM] |
| sorbose | linear | L-sorbose | [SOL] |
| pyranose | α-L-sorbopyranose | [SOE] | |
| allose | pyranose | β-D-allopyranose | [ALL] |
Amino sugars
[NDG] = α-GlcNAc = N-acetyl-α-D-glucosamine = 2-(acetylamino)-2-deoxy-α-D-glucopyranose
[NAG] = β-GlcNAc = N-acetyl-β-D-glucosamine = 2-(acetylamino)-2-deoxy-β-D-glucopyranose
[A2G] = α-GalNAc = N-acetyl-α-D-galactosamine = 2-(acetylamino)-2-deoxy-α-D-galactopyranose
[NGA] = β-GalNAc = N-acetyl-β-D-galactosamine = 2-(acetylamino)-2-deoxy-β-D-galactopyranose
Sugar alcohols
[MTL] = D-mannitol
[SOR] = D-glucitol = D-sorbitol
[XYL] = D-xylitol
Sugar acids
[GCU] = D-glucuronic acid = α-D-glucopyranuronic acid
[RHA] = 6-deoxy-mannose-1'-phosphate
[SIA] = α-NeuNAc = 5-N-acetyl-α-D-neuraminic acid
[SLB] = β-NeuNAc = 5-N-acetyl-β-D-neuraminic acid
[AMU] = N-acetyl-β-muramic acid
Disaccharides
[MAL] = maltose = [α-D-Glcp(1->4)]2
[CBI] = cellobiose = [β-D-Glcp(1->4)]2
[TRE] = trehalose = α-D-Glcp(1->1)α-D-Glcp
[MAB] = mannobiose = [β-D-Manp(1->4)]2
[LBT] = alpha-lactose = β-D-Galp(1->4)α-D-Glcp
[LAT] = beta-lactose = β-D-Galp(1->4)β-D-Glcp
[SUC] = sucrose = β-D-Fruf(2->1)α-D-Glcp
Trisaccharides
[MLR] = maltotriose = [α-D-Glcp(1->4)]3
[CTR] = cellotriose = [β-D-Glcp(1->4)]2α-D-Glcp
[CT3] = beta-cellotriose = [β-D-Glcp(1->4)]3
Tetrasaccharides
[MTT] = maltotetraose = [α-D-Glcp(1->4)]4
[CTT] = cellotetraose = [β-D-Glcp(1->4)]4
References
- RCSB PDB `Ligand Expo´ Chemical Component Search Tools
- [PDBe ligand dictionary https://www.ebi.ac.uk/pdbe-srv/pdbechem/]
